bluuebunny/crossref_metadata_2025 huggingface dataset:
Absence of Priming Coupled with Substantially Preserved Recognition in Lorazepam-Induced Amnesia
Authors: Brown Malcolm W. , Brown John , Bowes John B.
Published: September 2011

Two experiments are reported on priming when subjects are in an amnesic state induced by lorazepam. The primed tasks were completion of word-stems and generation of words from specified categories. In both experiments, lorazepam subjects showed no evidence of priming, whereas control subjects showed substantial priming. Recognition by the amnesic subjects of items produced in the priming tests, although impaired, was well above the chance level. These findings contrast with those obtained with organic amnesic subjects, for whom priming is typically normal but recognition is grossly impaired. The theoretical implications of this double dissociation between priming and recognition are discussed.
“Enacted” Auditory Images are Ambiguous; “Pure” Auditory Images are Not
Authors: Reisberg Daniel , Smith J. David , Baxter David A. , Sonenshine Marcia
Published: September 2011

Previous research indicates that visual images are inherently unambiguous. The present study extends this argument to auditory imagery. In Experiment 1, subjects were able to reinterpret an imaged ambiguous auditory figure, but covert subvocalization apparently aided this reinterpretation. When subvocalization was blocked, reinterpretations were eliminated. Experiments 2 and 3 generalize this finding to different procedures and stimuli. Experiment 4 explores further the role of subvocalization, by showing that the likelihood of reinterpreting an imaged stimulus is directly proportional to the degree of enactment allowed. We argue that subvocalization or enactment provides an internal stimulus that is subject to reinterpretation. Without enactment, the “pure” auditory image is as unambiguous as a visual image. Thus, in both visual and auditory modalities, images come into being as representations and so are inherently meaningful.
Modelling Visual Detection: Luminance Response Non-linearity and Internal Noise
Authors: Kingdom Fred , Moulden Bernard
Published: September 2011

Two experiments that investigate the effect of various display factors on the detectability of a thin line signal in random visual noise are described. Three statistical decision models are described, together with their ability to account for the results. The first is an “ideal detector” model, the second an “energy integrator” model, and the third a model based upon the operation of retinal ganglion cells which incorporates a gain control mechanism. The ideal detector model fails to give a good account of human performance, whereas the other two models provide a good fit to the data. The digital Laplacian with gain control model has the slight advantage over the energy integrating model in being able to account for a small superiority in the detection of dark as opposed to bright signals. Finally, both models require the inclusion of an estimate of the internal noise of the human visual system to account for the pattern of performance observed under changing conditions of display contrast.
Varieties of Object Constancy
Authors: Ellis R. , Allport D. A. , Humphreys G. W. , Collis J.
Published: September 2011

Three experiments are described in which two pictures of isolated man-made objects were presented in succession. The subjects’ task was to decide, as rapidly as possible, whether the two pictured objects had the same name. With a stimulus-onset asynchrony (SOA) of above 200 msec two types of facilitation were observed: (1) the response latency was reduced if the pictures showed the same object, even though seen from different viewpoints (object benefit); (2) decision time was reduced further if the pictures showed the same object from the same angle of view (viewpoint benefit). These facilitation effects were not affected by projecting the pictures to different retinal locations. Significant benefits of both types were also obtained when the projected images differed in size. However, in these circumstances there was a small but significant performance decrement in matching two similar views of a single object, but not if the views were different. Conversely, the object benefit, but not the viewpoint benefit, was reduced when the SOA was only 100 msec. The data suggest the existence of (at least) two different visual codes, one non-retinotopic but viewer-centred, the other object-centred.
Understanding Choice Utterances
Authors: Ray Jack L. , Reynolds Rodney A. , Carranza E.
Published: September 2011

When individuals offer choices, they intend them to be mandatory (requiring action) or permissive (not requiring action), and they intend them to be open (allowing the choice of both options) or closed (not allowing the choice of both options). In two studies subjects were presented with sets of syntactically equivalent disjunctive sentences with varying content designed to represent four patterns of permitted choice. The research indicates that individuals distinguish four distinct uses of “or” in deontic contexts, and that individuals more often judge choices as mandatory than permissive. The research also compared responses to questions about choice giver intent and receiver choice. The data indicate that when judging intent, individuals are inclined to understand some choices to be permissive. However, when judging what action they might take as choice receiver, subjects tend to regard action to be mandatory. It appears that although people have some facility in assessing a permission giver's intent, they often apply a more restrictive rule to themselves than is required by the choice giver.
Spreading Activation in Episodic Memory: Further Evidence for Age Independence
Authors: Balota David A. , Duchek Janet M.
Published: September 2011

Seventy-two young (mean age = 25 years) and 72 old adults (mean age = 71 years) participated in an experiment that addressed the influence of episodic and semantic prime activation on speeded episodic recognition judgements. On each test block, subjects studied two paragraphs at their own pace to achieve a designated level of episodic recognition performance. Following the study period, subjects were presented a series of prime–target trials for speeded episodic recognition. The primes were either (a) episodically related to the target, (b) semantically related to the target, (c) episodically and semantically related to the target, or (d) episodically and semantically unrelated to the target. The stimulus onset asynchrony (SOA) between the primes and targets was either 200 msec, 600 msec, or 1000 msec to address age-related changes in the rate at which these different prime types influenced performance. The results indicated that, compared to young adults, the old adults (a) studied the paragraphs for a longer period of time, (b) responded to the targets more slowly, and (c) were less accurate in their episodic recognition decisions. Although there were these main effects of age, the young and old adults were influenced in a similar fashion by the different prime-target relationships and by the interactive influences of the prime–target relationships and SOA. Correlational analyses indicated that the pattern of priming effects was as similar across the two age groups as across two pseudo-groups that were matched on the age dimension. These results were viewed as further support for the notion that the characteristics of the spreading activation mechanism as reflected by prime–target manipulations are relatively stable across young and old adults.
Critical Notice: Deadly Tenacity and Almost Diabolical Cunning
Authors: Smith Philip T.
Published: September 2011

This method taxes patience to the utmost, and could hardly have arisen in a country whose natives could be bored…. There is little of the grand style about these new prism, pendulum and chronograph-philosophers. They mean business, not chivalry. What generous divination, and that superiority in virtue which was thought by Cicero to give a man the best insight into nature, have failed to do, their spying and scraping, their deadly tenacity and almost diabolical cunning, will doubtless some day bring about. [James, 1890/1950, pp. 192–193]
The effect of semantic relatedness on immediate serial recall and serial recognition
Authors: Tse Chi-Shing , Li Yongna , Altarriba Jeanette
Published: September 2011

The present study examined the effects of semantic relatedness on immediate serial recall and serial recognition. Each participant received either blocked or randomly intermixed serial recall or serial recognition trials. Replicating the findings of previous studies (e.g., Saint-Aubin, Ouellette, & Poirier, 2005), semantic relatedness boosted percentage serial recall but also increased order errors, after taking into account the proportion of correctly recalled items, regardless of their orders, in serial recall trials. In serial recognition trials, participants’ responses were slower and less accurate for related lists than for unrelated lists. There were intraindividual correlations among order memory measures in serial recall versus serial recognition trials. The implications of these findings for item redintegration theories are discussed.
Functional analysis of the microtubule-interacting transcriptome
Authors: Sharp Judith A. , Plant Joshua J. , Ohsumi Toshiro K. , Borowsky Mark , Blower Michael D.
Published: September 2011

RNA localization is an important mechanism for achieving precise control of posttranscriptional gene expression. Previously, we demonstrated that a subset of cellular mRNAs copurify with mitotic microtubules in egg extracts of Xenopus laevis. Due to limited genomic sequence information available for X. laevis, we used RNA-seq to comprehensively identify the microtubule-interacting transcriptome of the related frog Xenopus tropicalis. We identified ∼450 mRNAs that showed significant enrichment on microtubules (MT-RNAs). In addition, we demonstrated that the MT-RNAs incenp, xrhamm, and tpx2 associate with spindle microtubules in vivo. MT-RNAs are enriched with transcripts associated with cell division, spindle formation, and chromosome function, demonstrating an overrepresentation of genes involved in mitotic regulation. To test whether uncharacterized MT-RNAs have a functional role in mitosis, we performed RNA interference and discovered that several MT-RNAs are required for normal spindle pole organization and γ-tubulin distribution. Together, these data demonstrate that microtubule association is one mechanism for compartmentalizing functionally related mRNAs within the nucleocytoplasmic space of mitotic cells and suggest that MT-RNAs are likely to contribute to spindle-localized mitotic translation.
inSilicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO
Authors: Taminau Jonatan , Steenhoff David , Coletta Alain , Meganck Stijn , Lazar Cosmin , de Schaetzen Virginie , Duque Robin , Molter Colin , Bersini Hugues , Nowé Ann , Weiss Solís David Y.
Published: September 2011

Microarray technology has become an integral part of biomedical research and increasing amounts of datasets become available through public repositories. However, re-use of these datasets is severely hindered by unstructured, missing or incorrect biological samples information; as well as the wide variety of preprocessing methods in use. The inSilicoDb R/Bioconductor package is a command-line front-end to the InSilico DB, a web-based database currently containing 86 104 expert-curated human Affymetrix expression profiles compiled from 1937 GEO repository series. The use of this package builds on the Bioconductor project's focus on reproducibility by enabling a clear workflow in which not only analysis, but also the retrieval of verified data is supported.

Availability: inSilicoDb is available as part of the Bioconductor project. There is a companion web interface that can be used for browsing available datasets before importing them into R/Bioconductor (http://insilico.ulb.ac.be).

Contact:  jtaminau@vub.ac.be
“Nullius in Bergmann” or the pluralistic approach to ecogeographical rules: a reply to Watt et al. (2010)
Authors: Olalla‐Tárraga Miguel Á.
Published: September 2011

Bergmann's rule is one of the best known empirical generalizations in biogeography and remains a topic of much interest and debate. Watt et al. claimed in 2010 that the only definition for the rule should be the one devised by Bergmann in the 19th‐century. Based on direct translations from the original German manuscript, they concluded that tests of the rule should be restricted to interspecific studies of body size variation in endotherms. Furthermore, they suggested that Bergmann's heat conservation mechanism is an integral part of the rule and, hence, a simple falsificationist test of this mechanism might be enough to validate the rule. Here I advocate on a pluralistic approach to study ecogeographical rules, in general, and Bergmann's rule in particular. Our perceptions on the status and validity of laws and rules depend on the narrowness of the epistemological scope we adopt. Laws can have exceptions, do not necessarily have to be explanatory and may not be predictive. Also, we should differentiate between correlative and causal laws. Bergmann's rule is a correlative law, not a causal law, as Watt et al. implicitly assumed. It is a broad generalization with no inherent mechanism, and subject to the scrutiny of empirical investigation. Because of the ecological and evolutionary contingencies there will hardly be any law in ecology that is universally true. We have to consider each of these contingencies and study Bergmann's rule in a diversity of systems, organisms and levels of biological organization to gain further insight into the processes underlying the geographic variation in body size. On the basis of the empirical evidence to date, we cannot entirely dismiss a thermoregulatory mechanism to explain body size clines in both ectotherms and endotherms and support a food availability mechanism instead, as Watt et al. suggested. Even so, a unifying explanation for Bergmann's rule still remains elusive.
Managing shame: An interpersonal perspective
Authors: Leeming Dawn , Boyle Mary
Published: September 2011

Experiences of shame are often difficult to manage, not least because of their interpersonal implications. However, limited research attention has been paid to the management and repair of shame, and in particular to the role that social factors may play in this. We aimed to explore these issues by obtaining 50 written first‐person accounts of experiences of managing difficult episodes of shame from a cross section of students and employees at a British university. These participant‐generated narrative accounts were supplemented by written answers to open‐ended questions. Via a contextual constructionist thematic analysis, three overarching themes were identified:The centrality of others’ evaluations of the self;Repositioning the self vis‐à‐vis others, andBeing disabled by shame. Discussion focuses on the first two of these themes which together suggest that because the participants saw their shame as produced in interaction with others, effective management and repair of shame depended not just on a changed view of the self but on a repositioning of the self in relation to others. This analysis therefore suggests that repair of shame may often need to be mutually negotiated and as such provides support for theoretical approaches to shame which emphasize the centrality of others’ actual or perceived judgements of the self.
Experimental Study of Effects of Operating Conditions on Water Transport Phenomena in the Cathode of Polymer Electrolyte Membrane Fuel Cell
Authors: Seo Sang Hern , Lee Chang Sik
Published: September 2011

Water management in polymer electrolyte membrane fuel cells is important because fuel cell performance may be lower when flooding emerges. In addition, the proton conductivity and water transport coefficient in the membrane depend on the hydration of the membrane. In this study a water transport phenomenon in the cathode channels of a polymer electrolyte membrane fuel cell was investigated under various operating conditions. To obtain images of the water the transparent fuel cell had a polycarbonate window installed at the cathode end plate, and gold-coated stainless steel was used for the flow field and current collector of the cathode. The effects of operating conditions on water transport manipulated operating parameters such as cell temperature, cathode flow rate, and cathode backpressure. As the operating time elapsed, it was observed that water droplet formation, growth, coalescence, and removal occurred in the cathode channel. It concluded that a high cathode flow rate prevented flooding by removing water from the cathode flow channel. Also, the quantity of water droplets increased with a high cathode backpressure.
Geometry and Mechanics in the Opening of Chiral Seed Pods
Authors: Armon Shahaf , Efrati Efi , Kupferman Raz , Sharon Eran
Published: September 2011

Two joined latex strips show complex twisting behavior similar to that of seed pods.
Single–Base Pair Unwinding and Asynchronous RNA Release by the Hepatitis C Virus NS3 Helicase
Authors: Cheng Wei , Arunajadai Srikesh G. , Moffitt Jeffrey R. , Tinoco Ignacio , Bustamante Carlos
Published: September 2011

During RNA unwinding, nucleotides are transiently sequestered, and their release is decoupled from base pair opening.
Disentangling the Drivers of β Diversity Along Latitudinal and Elevational Gradients
Authors: Kraft Nathan J. B. , Comita Liza S. , Chase Jonathan M. , Sanders Nathan J. , Swenson Nathan G. , Crist Thomas O. , Stegen James C. , Vellend Mark , Boyle Brad , Anderson Marti J. , Cornell Howard V. , Davies Kendi F. , Freestone Amy L. , Inouye Brian D. , Harrison Susan P. , Myers Jonathan A.
Published: September 2011

Increases in species turnover of woody plants at low latitudes and elevations are explained by the size of species pools alone.
Acceleration of Emergence of Bacterial Antibiotic Resistance in Connected Microenvironments
Authors: Zhang Qiucen , Lambert Guillaume , Liao David , Kim Hyunsung , Robin Kristelle , Tung Chih-kuan , Pourmand Nader , Austin Robert H.
Published: September 2011

Gradients of antibiotics generated in a microfluidic device provoke selection of ciprofloxacin resistance in
Escherichia coli
.
The Role of a Bilayer Interfacial Phase on Liquid Metal Embrittlement
Authors: Luo Jian , Cheng Huikai , Asl Kaveh Meshinchi , Kiely Christopher J. , Harmer Martin P.
Published: September 2011

The formation of single-layer complexes between different metals is a cause of liquid metal embrittlement.
Asynchronous Diversification in a Specialized Plant-Pollinator Mutualism
Authors: Ramírez Santiago R. , Eltz Thomas , Fujiwara Mikiko K. , Gerlach Günter , Goldman-Huertas Benjamin , Tsutsui Neil D. , Pierce Naomi E.
Published: September 2011

Insect sensory biases played a major role in driving reproductive adaptations in flowering plants.
Novel Multitarget Real-Time PCR Assay for Rapid Detection of Bordetella Species in Clinical Specimens
Authors: Tatti Kathleen M. , Sparks Kansas N. , Boney Kathryn O. , Tondella Maria Lucia
Published: September 2011

A novel multitarget real-time PCR (RT-PCR) assay for the rapid identification of
Bordetella pertussis
,
B. parapertussis
, and
B. holmesii
was developed using multicopy insertion sequences (ISs) in combination with the pertussis toxin subunit S1 (
ptxS
1
) singleplex assay. The RT-PCR targets for the multiplex assay include IS
481
, commonly found in
B. pertussis
and
B. holmesii
; IS
1001
of
B. parapertussis
; and the IS
1001
-like sequence of
B. holmesii
. Overall, 402
Bordetella
species and 66 non-
Bordetella
species isolates were tested in the multitarget assay. Cross-reactivity was found only with 5
B. bronchiseptica
isolates, which were positive with IS
1001
of
B. parapertussis
. The lower limit of detection (LLOD) of the multiplex assay was similar to the LLOD of each target in an individual assay format, which was approximately 1 genomic equivalent per reaction for all targets. A total of 197 human clinical specimens obtained during cough-illness outbreak investigations were used to evaluate the multitarget RT-PCR assay. The multiplex assay results from 87 clinical specimens were compared to the individual RT-PCR assay and culture results. The multitarget assay is useful as a diagnostic tool to confirm
B. pertussis
infections and to rapidly identify other
Bordetella
species. In conclusion, the use of this multitarget RT-PCR approach increases specificity, while it decreases the amount of time, reagents, and specimen necessary for RT-PCRs used for accurate diagnosis of pertussis-like illness.
Aortic Homograft Endocarditis Caused by Campylobacter jejuni
Authors: Dinant Sander , Schurink Carolina A. M. , Deckers Jaap W. , Severin Juliëtte A.
Published: September 2011

We report the first case of homograft endocarditis caused byCampylobacter jejuni, which was treated successfully with antibiotic therapy and valve replacement. To our knowledge, only two other cases ofC. jejuniendocarditis, involving native valves, have been reported in the medical literature.
Species Distribution of the Mycobacterium tuberculosis Complex in Clinical Isolates from 2007 to 2010 in Turkey: a Prospective Study
Authors: Bayraktar Banu , Bulut Emin , Barış Ayşe Bayrı , Toksoy Buket , Dalgıc Nazan , Celikkan Cigdem , Sevgi Dilek
Published: September 2011

The
Mycobacterium tuberculosis
complex (MTBC) consists of a group of closely related species that differ in their epidemiological profiles, host ranges, pathogenicities, geographic distributions, and drug resistances. Identification of members in the MTBC is essential for monitoring the epidemiology of tuberculosis (TB) and implementing appropriate public health control measures. In this study, 188 consecutive MTBC clinical isolates from 2007 to 2010 were evaluated to determine the prevalence of MTBC species in Turkey. PCR and restriction fragment length polymorphism analysis (PCR-RFLP) of the
gyrB
gene were used, and results for species other than
M. tuberculosis
were confirmed using the GenoType MTBC assay (Hain Lifescience, Nehren, Germany). Most of the strains were found to be
M. tuberculosis
(94.1%). The prevalences of
M. bovis
and
M. caprae
were 4.3% and 1.6%, respectively. Only one
M. bovis
BCG strain was identified. Overall, the frequency of bovine tuberculosis in humans was 5.3%. We had assumed that bovine TB infection was under control in animal herds, but primary
M. bovis
infections in humans caused by transmission from infected animals are still an issue in Turkey. Our results indicate that the frequent identification of
M. bovis
in routine mycobacteriological laboratory work has further importance due to the well-known resistance of this species to pyrazinamide.
Autographa californica Multiple Nucleopolyhedrovirus GP64 Protein: Roles of Histidine Residues in Triggering Membrane Fusion and Fusion Pore Expansion
Authors: Li Zhaofei , Blissard Gary W.
Published: September 2011

The
Autographa californica
multiple nucleopolyhedrovirus (AcMNPV) GP64 protein mediates membrane fusion during entry. Fusion results from a low-pH-triggered conformational change in GP64 and subsequent interactions with the membrane bilayers. The low-pH sensor and trigger of the conformational change are not known, but histidine residues are implicated because the pK
a
of histidine is near the threshold for triggering fusion by GP64. We used alanine substitutions to examine the roles of all individual and selected clusters of GP64 histidine residues in triggering and mediating fusion by GP64. Three histidine residues (H152, H155, and H156), located in fusion loop 2, were identified as important for membrane fusion. These three histidine residues were important for efficient pore expansion but were not required for the pH-triggered conformational change. In contrast, a cluster of three histidine residues (H245, H304, and H430) located near the base of the central coiled coil was identified as a putative sensor for low pH. Three alanine substitutions in cluster H245/H304/H430 resulted in dramatically reduced membrane fusion and the apparent loss of the prefusion conformation at neutral pH. Thus, the H245/H304/H430 cluster of histidines may function or participate as a pH sensor by stabilizing the prefusion structure of GP64.
Residues of the Human Metapneumovirus Fusion (F) Protein Critical for Its Strain-Related Fusion Phenotype: Implications for the Virus Replication Cycle
Authors: Mas Vicente , Herfst Sander , Osterhaus Albert D. M. E. , Fouchier Ron A. M. , Melero José A.
Published: September 2011

The paramyxovirus F protein promotes fusion of the viral and cell membranes for virus entry, as well as cell-cell fusion for syncytium formation. Most paramyxovirus F proteins are triggered at neutral pH to initiate membrane fusion. Previous studies, however, demonstrated that human metapneumovirus (hMPV) F proteins are triggered at neutral or acidic pH in transfected cells, depending on the strain origin of the F sequences (S. Herfst et al., J. Virol. 82:8891–8895, 2008). We now report an extensive mutational analysis which identifies four variable residues (294, 296, 396, and 404) as the main determinants of the different syncytial phenotypes found among hMPV F proteins. These residues lie near two conserved histidines (H368 and H435) in a three-dimensional (3D) model of the pretriggered hMPV F trimer. Mutagenesis of H368 and H435 indicates that protonation of these histidines (particularly His435) is a key event to destabilize the hMPV F proteins that require low pH for cell-cell fusion. The syncytial phenotypes were reproduced in cells infected with the corresponding hMPV strains. However, the low-pH dependency for syncytium formation could not be related with a virus entry pathway dependent on an acidic environment. It is postulated that low pH may be acting for some hMPV strains as certain destabilizing mutations found in unusual strains of other paramyxoviruses. In any case, the results presented here and those reported by Schowalter et al. (J. Virol. 83:1511–1522, 2009) highlight the relevance of certain residues in the linker region and domain II of the pretriggered hMPV F protein for the process of membrane fusion.
The Virion Host Shutoff Protein of Herpes Simplex Virus 1 Blocks the Replication-Independent Activation of NF-κB in Dendritic Cells in the Absence of Type I Interferon Signaling
Authors: Cotter Christopher R. , Kim Won-keun , Nguyen Marie L. , Yount Jacob S. , López Carolina B. , Blaho John A. , Moran Thomas M.
Published: September 2011

Immune evasion is a defining feature of the virus-host relationship. During infection, herpes simplex virus type 1 (HSV-1) utilizes multiple proteins to manipulate the host immune response. In the present study, we investigated the mechanism by which the virion host shutoff (vhs) protein blocks the activation of dendritic cells (DCs). Previously, we found that coinfection of wild-type HSV-1 with a panel of RNA viruses resulted in a block to DC activation that was attributable to vhs. These observations led us to hypothesize that the vhs-mediated inhibition was dependent on signaling through the RIG-I-like receptor (RLR) signaling pathway. By examining DCs generated from MAVS (IPS-1) knockout (KO) mice, we determined that RLR/MAVS signaling is not essential for the DC response to HSV-1. We also evaluated the requirement for the type I interferon (IFN) signaling pathway in DC activation following infection with HSV-1 and found that stimulation of DCs with wild-type HSV-1 required intact type I IFN signaling for the production of cytokines, whereas the vhs deletion (vhs
−
) mutant virus activated DCs without the need for exogenous IFN signaling. Comparisons of transcription factor activation in DCs infected with wild-type HSV and the vhs
−
mutant virus revealed that NF-κB activation was inhibited by vhs in the early phase of the infection. In contrast, IRF3 activation was not influenced by vhs. In these studies, measurement of proinflammatory cytokines and type I IFN release from the infected DCs reflected the activation status of these transcription factors. Taken together, the work presented here (i) describes a novel role for the vhs protein as an inhibitor of the early activation of NF-κB during HSV-1 infection of DCs and (ii) offers a mechanistic explanation of how this protein interferes with DC activation.
Rotavirus Infection Induces the Unfolded Protein Response of the Cell and Controls It through the Nonstructural Protein NSP3
Authors: Trujillo-Alonso Vicenta , Maruri-Avidal Liliana , Arias Carlos F. , López Susana
Published: September 2011

The unfolded protein response (UPR) is a cellular mechanism that is triggered in order to cope with the stress caused by the accumulation of misfolded proteins in the endoplasmic reticulum (ER). This response is initiated by the endoribonuclease inositol-requiring enzyme 1 (IRE1), activating transcription factor 6 (ATF6), and PKR-like ER kinase, which increase the expression of the genes involved in the folding and degradation processes and decrease the protein input into the ER by inhibiting translation. It has been shown that viruses both induce and manipulate the UPR in order to protect the host cells from an ER stress-mediated death, thus permitting the translation of viral proteins and the efficient replication of the virus. To understand the cellular events that occur during the rotavirus replication cycle, we examined the activation of the three UPR arms following infection, using luciferase reporters driven by promoters of the ER stress-responsive genes and real-time reverse transcription-PCR to determine the levels of the stress-induced mRNAs. Our findings indicated that during rotavirus infection two of the three arms of the UPR (IRE1 and ATF6) become activated; however, these pathways are interrupted at the translational level by the general inhibition of protein synthesis caused by NSP3. This response seems to be triggered by more than one viral protein synthesized during the replication of the virus, but not by the viral double-stranded RNA (dsRNA), since cells transfected with psoralen-inactivated virions, or with naked viral dsRNA, did not induce UPR.
Problems with a conformation assignment of aryl-substituted resorc[4]arenes
Authors: Kaminský Jakub , Dvořáková Hana , Štursa Jan , Moravcová Jitka
Published: September 2011

Acid-catalyzed condensation of resorcinol with 3,5-diisopropoxybenzaldehyde and 3,5-dihydroxybenzaldehyde afforded aryl substituted resorc[4]arenes 1a and 1b, respectively. All 16 hydroxyls in 1b were acetylated providing resorc[4]arene 1c. The conformational behaviour of 1a, 1b and 1c was studied by NMR spectroscopy and quantum chemical calculations. It was found that the stabilization of their conformations is an effect of competing π-π and OH-π interactions, hydrogen bonding and steric features, respectively. As a result, C2 symmetrical boat conformations 1a, 1b and 1c with aryls in axial positions were identified in all cases. In case of 1c also the formation of C2 symmetrical conformation with aryls in equatorial positions (boat-eq) was identified. Moreover, compounds 1a and 1b being able to create hydrogen bonds, adopt also symmetrical C4 crown conformations. For 1c(boat-ax), the boat-boat conversion with energy barrier of 80 kJ/mol was observed, while the 1c(boat-eq) was found to be rigid in the whole accessible temperature range. Both conformers of 1c exhibit also second dynamic process – rotation of bridge aryl rings (ΔG‡ = 66 kJ/mol).
A placental chorionic villous mesenchymal core cellular origin for infantile haemangioma
Authors: Itinteang Tinte , Tan Swee T , Guthrie Siobhan , Tan Cherise E S , McIntyre Ben C , Brasch Helen D , Day Darren J
Published: September 2011

Aims

To investigate the expression of the placental cell-specific associated proteins in infantile haemangioma (IH).

Methods

Immunohistochemical staining was used to investigate the expression of human chorionic gonadotrophin (hCG), human placental lactogen (hPL), human leucocyte antigen-G (HLA-G), cytokeratin 7 (CK7) and smooth muscle actin in paraffin-embedded sections of proliferating and involuted IHs.

Results

The proteins hCG and hPL were expressed by the endothelium but not the pericyte layer of proliferating IH, but these proteins were not detected in involuted lesions. There was no expression of CK7 and HLA-G in IH.

Conclusions

The expression of hCG and hPL, but not CK7 or HLA-G, by the endothelium of proliferating IH supports a placental chorionic villous mesenchymal core cellular origin for IH rather than a trophoblast origin.
A syllabus for research ethics committees: training needs and resources in different European countries
Authors: Cairoli Ester , Davies Hugh T , Helm Jürgen , Hook Georg , Knupfer Petra , Wells Frank
Published: September 2011

This paper reports a European Forum for Good Clinical Practice workshop held in 2011 to consider a research ethics committee training syllabus, subsequent training needs and resources. The syllabus that was developed was divided into four competencies: committee working; scientific method; ethical analysis and the regulatory framework. Appropriate training needs for each, with possible resources, were discussed. Lack of funding for training was reported as a major problem but affordable alternatives were debated. Strengths and weaknesses of this approach were discussed and the resultant proposal will be disseminated through the European Forum for Good Clinical Practice and the research ethics committees of member states.
GEOMETRIC IIA SUPERGRAVITY THEORIES IN THE STRING FRAME
Authors: NICOLETTI RICCARDO , ORAZI EMANUELE
Published: September 2011

Using the geometric (rheonomic) approach based on the Free Differential Algebra, we derive the full type IIA D = 10 supergravity Lagrangian in the string frame, including the Romans' mass deformation, and containing the explicit four-fermion interactions, absent from the original Romans' paper. This provides a deeper insight into the group theoretical and algebraic structures of the theory. Moreover we provide the full set of supersymmetry transformation laws both in the Romans'-deformed and undeformed theories. The structure of the bosonic Free Differential Algebra for the HLW deformation is also presented.
Crystalline In–Ga–Zn–O Density of States and Energy Band Structure Calculation Using Density Function Theory
Authors: Chen Charlene , Cheng Kai-Chen , Chagarov Evgeniy , Kanicki Jerzy
Published: September 2011

The density of states (DOS) and energy band structure of crystalline In–Ga–Zn–O (c-IGZO) and the impact of point defects on its electronic structure are investigated by first-principles calculations based on the density function theory. The calculated DOS showed that the p-orbitals of the oxygen atoms mostly contribute to the valance band maximum (VBM) of c-IGZO. The conduction band minimum (CBM) is dominated by s-orbitals of the Zn/Ga mixture atoms, while the In atoms have the largest spatial spread of wave function. Oxygen vacancies create fully occupied defect states within the band gap and serve as deep donors. Both hydrogen substitutions and interstitials act like shallow donors, and raise the Fermi level above the CBM. Oxygen split interstitials created fully occupied defect states above VBM, while oxygen octahedral interstitials create both occupied and unoccupied states, and may serve as acceptors.
Palladium–Hydrogen Complex in Silicon Observed by Electron Spin Resonance Measurement
Authors: Ishiyama Takeshi , Kimura Shutaro , Mori Yuya , Kamiura Yoichi , Yamashita Yoshifumi
Published: September 2011

We have investigated a palladium–hydrogen complex in silicon by electron spin resonance (ESR) measurement. A new ESR spectrum was detected in a sample diffused with palladium and hydrogen. The hyperfine structure of hydrogen atoms in the ESR spectrum shows that the spectrum originates from a palladium–hydrogen complex containing three hydrogen atoms (Pd–H3). The anisotropic g-value of Pd–H3 shows that the Pd–H3 complex has an anisotropic character of orthorhombic (C
2v
) symmetry. The calculated g-values of the Pd–H3 complex are g
1 = 2.12, g
2 = 2.10, and g
3 = 2.03, and the g
2 axis is along the <100 > direction. The anisotropic character of orthorhombic (C
2v
) symmetry results from a configuration consisting of one Pd atom at a substitutional site, two equivalent hydrogen atoms at interstitial sites along the <111 > direction, and one hydrogen atom at the next-nearest-neighbor interstitial site along the <100 >-twofold symmetry axis. We have also studied the dissociation of a platinum–hydrogen complex by thermal treatment. The activation energy for the dissociation of the Pd–H3 complex is estimated to be about 1.6 eV.
Experimental and Simulation Studies of Solid-Phase Crystallization of Fluorine-Implanted Amorphous Silicon on Silicon Dioxide
Authors: Ma Chia-Chi , Hsieh Fu-Han , Wu Yeh-Wei , Chang Ruey-Dar
Published: September 2011

In this study, we investigated how fluorine implantation affects the crystallization of amorphous silicon (a-Si) prepared by low-pressure chemical vapor deposition. Fluorine and silicon ions were implanted at the center of the a-Si and a-Si/SiO2 interface to identify whether the effect is caused by implantation damage or fluorine incorporation into the thin film. Two-dimensional Monte-Carlo simulation was performed to clarify crystallization mechanisms. The microstructures obtained experimentally were reproduced by the simulation. Experimental and simulation results indicate that damage caused by fluorine implanted at the a-Si/SiO2 interface increased the energy barrier to stable nuclei formation, causing a significant reduction in the nucleation rate. Fluorine incorporation into the a-Si film reduced the growth rate as fluorine was implanted at the film center.
Phase Evolution and Nucleus Growth Observation of Solid-State BaTiO3 Powder Prepared by High-Energy Bead Milling for Raw Material Mixing
Authors: Lee Ting-Tai , Huang Chi-Yuen , Chang Che-Yuan , Lin Shih-Pin , Su Che-Yi , Lee Chun-Te , Fujimoto Masayuki
Published: September 2011

The solid-state synthesis, phase evolution, and nucleus growth of the barium titanate (BaTiO3, BT) powder were investigated in this study. Rapid nucleus growth and precursor phase formation of BT were observed at a relatively low temperature of 600 °C by mixing BaCO3 (2 m2/g) and TiO2 (7 m2/g) with a high-energy bead mill. The decomposition of BaCO3 and the formation of the Ba2TiO4 phase were identified by transmission electron microscopy (TEM). On the basis of this observation, the weight loss observed at 600 °C in the derivative thermogravimetry (DTG) curve could also be explained. Furthermore, with increasing calcination temperature, single cubic BT with less than 80 nm fine nuclei/crystallites was observed at 900 °C, and tetragonal BT (c/a > 1.008) with an average particle size of 0.4 µm was obtained at 1000 °C. With regard to the dielectric properties of sintered ceramics, the relative permittivity (εr) increased with calcination temperature, and the Curie point also shifted to a progressively higher temperature. However, BT nucleus samples (with low calcination temperatures of 800 and 900 °C) could not satisfy the X7R requirement (Electric Industries Association Standard, the tolerance of capacitance from -55 to +125 °C is ±15%) until calcination temperature increased to 1000 °C.
Measuring the Junction Temperature of GaInP/GaInAs/Ge Multijunction Solar Cells Using Photoluminescence
Authors: Shu Gia-Wei , Tung Chiun-Hsiang , Tung Shr-Chang , Su Po-Chen , Shen Ji-Lin , Yang Min-De , Wu Chih-Hung , Chou Wu-Ching , Ko Cheng-Hao
Published: September 2011

The junction temperatures of the three individual subcells of InGaP/InGaAs/Ge solar cells were measured using photoluminescence (PL) with three different excitation lasers. With the illumination of an extra xenon–mercury lamp, the linear relationship between the PL energy and the illumination level is clearly observed and advantageously used for deriving the junction temperature. Using the Varshni relationship between the PL peak energy and the heat-sink temperature allows us to determine the junction temperature in each subcell.
Super-Resolution Digital Holographic Microscopy for Three Dimensional Sample Using Multipoint Light Source Illumination
Authors: Phan Anh-Hoang , Park Jae-Hyeung , Kim Nam
Published: September 2011

In this paper, we use multipoint light source illumination to enhance the resolution of digital holographic microscopy. The specimen is sequentially illuminated from many directions by using multipoint light sources which are created by a lens-array. The high spatial frequency information of the specimen is directed to the limited numerical aperture of the objective lens and captured at a fixed position of image sensor. The three-dimensional information of the specimen can be reconstructed with enhanced resolution by reconstructing the captured holograms.
Design and Finite Element Method Analysis of Laterally Actuated Multi-Value Nano Electromechanical Switches
Authors: Kloub Hussam A. , Smith Casey E. , Hussain Muhammad M.
Published: September 2011

We report on the design and modeling of novel nano electromechanical switches suitable for implementing reset/set flip-flops, AND, NOR, and XNOR Boolean functions. Multiple logic operations can be implemented using only one switching action enabling parallel data processing; a feature that renders this design competitive with complementary metal oxide semiconductor and superior to conventional nano-electromechanical switches in terms of functionality per device footprint. The structural architecture of the newly designed switch consists of a pinned flexural beam structure which allows low strain lateral actuation for enhanced mechanical integrity. Reliable control of on-state electrical current density is achieved through the use of metal-metal contacts, true parallel beam deflection, and lithographically defined contact area to prevent possible device welding. Dynamic response as a function of device dimensions numerically investigated using ANSYS and MatLab Simulink.
Simple Method of Synthesizing Nickel–Nitrilotriacetic Acid Gold Nanoparticles with a Narrow Size Distribution for Protein Labeling
Authors: Kitai Toshiyuki , Watanabe Yuta , Toyoshima Yoko Y. , Kobayashi Takuya , Murayama Takashi , Sakaue Hiroyuki , Suzuki Hitoshi , Takahagi Takayuki
Published: September 2011

We developed a simple method to synthesize nickel–nitrilotriacetic acid gold nanoparticles (Ni–NTA Au NPs) with a narrow size distribution for site-specific labeling in protein complexes. Au NPs were synthesized by the reduction of HAuCl4 using trisodium citrate and tannin acid. Then, the nanoparticle surfaces were modified with NTA and subsequent complexation with Ni2+. The mean diameter of the synthesized Ni–NTA Au NPs was 4.3 nm, and the coefficient of variation was 9%. The specific binding of the Ni–NTA Au NPs to polyhistidine-tagged (His-tagged) proteins was determined by transmission electron microscopy using kinesin and the p62 subunit of dynactin. Consequently, our method is useful for analyzing the substructures of protein complexes.
Fixation of Surface-Modified Polydiacetylene Nano/Microcrystals on Substrates
Authors: Kinemuchi Takahiro , Moritani Yuto , Tatewaki Yoko , Okada Shuji
Published: September 2011

Polydiacetylene nanocrystals (NCs) and fibrous microcrystals (FMCs), whose surfaces were modified by carboxyl groups, were prepared by radical-initiator-induced solid-state polymerization of NCs and FMCs of 1,6-di(N-carbazolyl)-2,4-hexadiyne using 2,2'-azobis2-[N-(2-carboxylethyl)amidino]propane. The NCs and FMCs could be attached to glass substrates modified by amino groups when the glass substrates were immersed into NC and FMC dispersions of N,N-dimethylformamide. However, the adhesive force was weak and the ultrasonic treatment almost removed the NCs and FMCs. On the other hand, after heat treatment of the NCs and FMCs weakly bonded on the glass substrates, we found that 81% of the NCs and 56% of the FMCs remained on the substrates after sonication. The annealing process seemed to accelerate the condensation reaction between crystals and the substrates to form covalent bonds.
Accuracy Improvement for Light-Emitting-Diode-Based Colorimeter by Iterative Algorithm
Authors: Yang Pao-Keng
Published: September 2011

We present a simple algorithm, combining an interpolating method with an iterative calculation, to enhance the resolution of spectral reflectance by removing the spectral broadening effect due to the finite bandwidth of the light-emitting diode (LED) from it. The proposed algorithm can be used to improve the accuracy of a reflective colorimeter using multicolor LEDs as probing light sources and is also applicable to the case when the probing LEDs have different bandwidths in different spectral ranges, to which the powerful deconvolution method cannot be applied.
Applications of the Heterojunction with Intrinsic Thin Layer Solar-Cell Structure on Photodetectors
Authors: Wei Chun-You , Lin Chu-Hsuan
Published: September 2011

We have utilized the high-efficiency heterojunction with intrinsic thin-layer (HIT) solar-cell structure for applications in photodetectors. In this research, we have investigated the relationship between responsivities and thicknesses of active layers, including top intrinsic amorphous Si and bulk crystalline Si. The thickness of a HIT photodetector should depend on the detection wavelength desired. For a typical HIT structure with a 5-nm-thick top intrinsic amorphous Si layer, the responsivities at 450, 650, and 850 nm wavelengths could be 0.511, 0.529, and 0.641 A/W, respectively. The responsivity at the 450 nm wavelength can reach 0.591 A/W for a 20-nm-thick top intrinsic amorphous Si layer even when the bulk Si is only 1.5 µm thick.
Error-Correcting 6/8 Modulation Code for Reducing Two-Dimensional Intersymbol Interference
Authors: Kim Jinyoung , Lee Jaejin
Published: September 2011

We introduce error-correcting 6/8 modulation codes for reducing two-dimensional intersymbol interference in holographic data storage. The proposed modulation codes have a trellis-like structure in which the data is encoded, enabling their error-correcting capability, and are more complex than previous error-correcting 4/6 modulation codes because of increasing number of symbols and states compared to the conventional 6/8 modulation codes. The bit error rate (BER) performances are improved for the proposed modulation codes compared with those for 4/6 modulation codes, moreover the proposed codes make 12.5% times more efficient.
Perfect Tracking Control System with Prediction State Observer for Next-Generation Optical Disks
Authors: Ogata Tokoku , Nabata Yuta , Ohishi Kiyoshi , Miyazaki Toshimasa , Sazawa Masaki , Koide Daiichi , Takano Yoshimichi , Tokumaru Haruki
Published: September 2011

Recently, the capacity of optical disk recording systems has been increasing. Optical disk drive systems must realize high-precision tracking control. For this purpose, we previously proposed a tracking control system that is composed of both a robust feedback controller and a zero-phase-error feedforward tracking controller. The proposed feedforward tracking control system effectively suppresses the tracking error caused by track eccentricity. However, it is sometimes difficult for conventional feedforward tracking control systems to realize higher precision in their tracking control. Hence, in this paper we propose a new perfect tracking control (PTC) system with a prediction state observer for next-generation optical disks. The experimental results confirm that the proposed system suppresses the tracking error at a disk rotation speed of 8000 rpm. Therefore, the proposed system realizes high-precision tracking control.