bluuebunny/crossref_metadata_2025 huggingface dataset:
Making the H-Cluster from Scratch
Authors: Pickett Christopher J.
Published: January 2014

Spectroscopic data begin to elucidate the initial steps in the biosynthesis of the hydrogenase active site.

[Also see Report by

Kuchenreuther
et al.

]
Raw Personal Data: Providing Access
Authors: Lunshof Jeantine E. , Church George M. , Prainsack Barbara
Published: January 2014

Donors should have access to raw data derived from their contributions to research or clinical repositories to increase personal choice and reciprocity.
mRNA, Live and Unmasked
Authors: Akbalik Güney , Schuman Erin M.
Published: January 2014

Visualization of mRNA dynamics in live neurons reveals its release from granules at synapses during neuronal plasticity.

[Also see Reports by

Buxbaum
et al.

and

Park
et al.

]
Challenges for New ERC President
Authors: Boyle Paul
Published: January 2014

This month, Jean-Pierre Bourguignon began his tenure as president of the European Research Council (ERC). This is a daunting task for many reasons: The growing ERC budget requires that it be carefully positioned within a complex array of European funding opportunities; embedding the presidential role into the ERC executive agency in the European Commission's Directorate-General for Research and Innovation potentially reduces ERC's independence; and variable success rates for acquiring ERC funding are concerning, and research expectations will need to be managed.
Divulging DNA Secrets of Dead Stirs Debate
Authors: Couzin-Frankel Jennifer
Published: January 2014

Genetic findings from research volunteers who die present a conundrum, and there's debate over how to handle that information.
VgrG-5 Is a Burkholderia Type VI Secretion System-Exported Protein Required for Multinucleated Giant Cell Formation and Virulence
Authors: Schwarz Sandra , Singh Pragya , Robertson Johanna D. , LeRoux Michele , Skerrett Shawn J. , Goodlett David R. , West T. Eoin , Mougous Joseph D.
Published: January 2014

The type VI secretion system (T6SS) has emerged as a critical virulence factor for the group of closely related
Burkholderia
spp. that includes
Burkholderia pseudomallei
,
B. mallei
, and
B. thailandensis
. While the genomes of these bacteria, referred to as the Bptm group, appear to encode several T6SSs, we and others have shown that one of these, type VI secretion system 5 (T6SS-5), is required for virulence in mammalian infection models. Despite its pivotal role in the pathogenesis of the Bptm group, the effector repertoire of T6SS-5 has remained elusive. Here we used quantitative mass spectrometry to compare the secretome of wild-type
B. thailandensis
to that of a mutant harboring a nonfunctional T6SS-5. This analysis identified VgrG-5 as a novel secreted protein whose export depends on T6SS-5 function. Bioinformatics analysis revealed that VgrG-5 is a specialized VgrG protein that harbors a C-terminal domain (CTD) conserved among Bptm group species. We found that a
vgrG-5
ΔCTD mutant is avirulent in mice and is unable to stimulate the fusion of host cells, a hallmark of the Bptm group previously shown to require T6SS-5 function. The singularity of VgrG-5 as a detected T6SS-5 substrate, taken together with the essentiality of its CTD for virulence, suggests that the protein is critical for the effector activity of T6SS-5. Intriguingly, we show that unlike the bacterial-cell-targeting T6SSs characterized so far, T6SS-5 localizes to the bacterial cell pole. We propose a model whereby the CTD of VgrG-5—, propelled by T6SS-5—, plays a key role in inducing membrane fusion, either by the recruitment of other factors or by direct participation.
Role of Urinary Cathelicidin LL-37 and Human β-Defensin 1 in Uncomplicated Escherichia coli Urinary Tract Infections
Authors: Nielsen Karen L. , Dynesen Pia , Larsen Preben , Jakobsen Lotte , Andersen Paal S. , Frimodt-Møller Niels
Published: January 2014

Cathelicidin (LL-37) and human β-defensin 1 (hBD-1) are important components of the innate defense in the urinary tract. The aim of this study was to characterize whether these peptides are important for developing uncomplicated
Escherichia coli
urinary tract infections (UTIs). This was investigated by comparing urinary peptide levels of UTI patients during and after infection to those of controls, as well as characterizing the fecal flora of participants with respect to susceptibility to LL-37 and
in vivo
virulence. Forty-seven UTI patients and 50 controls who had never had a UTI were included. Participants were otherwise healthy, premenopausal, adult women. LL-37 MIC levels were compared for fecal
E. coli
clones from patients and controls and were also compared based on phylotypes (A, B1, B2, and D).
In vivo
virulence was investigated in the murine UTI model by use of selected fecal isolates from patients and controls. On average, UTI patients had significantly more LL-37 in urine during infection than postinfection, and patient LL-37 levels postinfection were significantly lower than those of controls. hBD-1 showed similar urine levels for UTI patients and controls. Fecal
E. coli
isolates from controls had higher LL-37 susceptibility than fecal and UTI
E. coli
isolates from UTI patients.
In vivo
studies showed a high level of virulence of fecal
E. coli
isolates from both patients and controls and showed no difference in virulence correlated with the LL-37 MIC level. The results indicate that the concentration of LL-37 in the urinary tract and low susceptibility to LL-37 may increase the likelihood of UTI in a complex interplay between host and pathogen attributes.
Real-Time Cellular Analysis Coupled with a Specimen Enrichment Accurately Detects and Quantifies Clostridium difficile Toxins in Stool
Authors: Huang Bin , Jin Dazhi , Zhang Jing , Sun Janet Y. , Wang Xiaobo , Stiles Jeffrey , Xu Xiao , Kamboj Mini , Babady N. Esther , Tang Yi-Wei
Published: January 2014

We describe here the use of an immunomagnetic separation enrichment process coupled with a modified real-time cellular analysis (RTCA) system (RTCA version 2) for the detection of
C. difficile
toxin (CDT) in stool. The limit of CDT detection by RTCA version 2 was 0.12 ng/ml. Among the consecutively collected 401 diarrheal stool specimens, 53 (13.2%) were toxin-producing
C. difficile
strains by quantitative toxigenic culture (qTC); bacterial loads ranged from 3.00 × 10
1
to 3.69 × 10
6
CFU/ml. The RTCA version 2 method detected CDT in 51 samples, resulting in a sensitivity of 96.2%, a specificity of 99.7%, and positive and negative predictive values of 98.1% and 99.4%, respectively. The positive step time ranged from 1.43 to 35.85 h, with <24 h for 80% of the samples. The CDT concentrations in stool samples determined by RTCA version 2 correlated with toxigenic
C. difficile
bacterial load (
R
2
= 0.554,
P
= 0.00002) by qTC as well as the threshold cycle (
R
2
= 0.343,
P
= 0.014) by real-time PCR. A statistically significant correlation between the CDT concentrations and the clinical severity of CDI was observed (
P
= 0.015). The sensitivity of the RTCA version 2 assay for the detection of functional toxins in stool specimens was significantly improved when the immunomagnetic separation enrichment process was incorporated. More than 80% positive results can be obtained within 24 h. The stool specimen CDT concentration derived using the RTCA version 2 assay correlates with clinical severity and may be used as a marker for monitoring the status of CDI.
Evaluation of Four Single-Locus Markers for Leishmania Species Discrimination by Sequencing
Authors: Van der Auwera Gert , Ravel Christophe , Verweij Jaco J. , Bart Aldert , Schönian Gabriele , Felger Ingrid
Published: January 2014

Several genetic markers have been described for discriminating
Leishmania
species. In most reported cases, one or a few polymorphisms are the basis of species identification, and the methods were validated on a limited number of strains from a particular geographical region. Therefore, most techniques may underestimate the global intraspecies variability and are applicable only in certain areas. In addition, interlaboratory standardization is mostly absent, complicating comparisons among different studies. Here, we compared species typing results from all sequence polymorphisms found in four popular markers that can be applied directly on clinical samples: the miniexon or spliced leader, the internal transcribed spacer of the ribosomal DNA array, the 7SL RNA gene, and the heat shock protein 70 gene. Clustering was evaluated among 74
Leishmania
strains, selected to represent a wide geographic distribution and genetic variability of the medically relevant species of the genus. Results were compared with a multilocus sequence typing (MLST) approach using 7 single-copy household genes and with multilocus enzyme electrophoresis (MLEE), still considered the gold standard by some. We show that strain groupings are highly congruent across the four different single-locus markers, MLST, and MLEE. Overall, the heat shock protein 70 gene and the miniexon presented the best resolutions for separating medically relevant species. As gene sequence analysis is validated here on a global scale, it is advocated as the method of choice for use in genetic, clinical, and epidemiological studies and for managing patients with unknown origins of infection, especially in Western infectious disease clinics dealing with imported leishmaniasis.
Misidentification of Aspergillus nomius and Aspergillus tamarii as Aspergillus flavus: Characterization by Internal Transcribed Spacer, β-Tubulin, and Calmodulin Gene Sequencing, Metabolic Fingerprinting, and Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Tam Emily W. T. , Chen Jonathan H. K. , Lau Eunice C. L. , Ngan Antonio H. Y. , Fung Kitty S. C. , Lee Kim-Chung , Lam Ching-Wan , Yuen Kwok-Yung , Lau Susanna K. P. , Woo Patrick C. Y.
Published: January 2014

Aspergillus nomius
and
Aspergillus tamarii
are
Aspergillus
species that phenotypically resemble
Aspergillus flavus
. In the last decade, a number of case reports have identified
A. nomius
and
A. tamarii
as causes of human infections. In this study, using an internal transcribed spacer, β-tubulin, and calmodulin gene sequencing, only 8 of 11 clinical isolates reported as
A. flavus
in our clinical microbiology laboratory by phenotypic methods were identified as
A. flavus
. The other three isolates were
A. nomius
(
n
= 2) or
A. tamarii
(
n
= 1). The results corresponded with those of metabolic fingerprinting, in which the
A. flavus
,
A. nomius
, and
A. tamarii
strains were separated into three clusters based on ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC MS) analysis. The first two patients with
A. nomius
infections had invasive aspergillosis and chronic cavitary and fibrosing pulmonary and pleural aspergillosis, respectively, whereas the third patient had
A. tamarii
colonization of the airway. Identification of the 11 clinical isolates and three reference strains by matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) showed that only six of the nine strains of
A. flavus
were identified correctly. None of the strains of
A. nomius
and
A. tamarii
was correctly identified. β-Tubulin or the calmodulin gene should be the gene target of choice for identifying
A. flavus
,
A. nomius
, and
A. tamarii
. To improve the usefulness of MALDI-TOF MS, the number of strains for each species in MALDI-TOF MS databases should be expanded to cover intraspecies variability.
Empyema Caused by Prevotella bivia Complicating an Unusual Case of Spontaneous Chylothorax
Authors: Di Marco Berardino Alessandro , Inchingolo Riccardo , Smargiassi Andrea , Re Antonina , Torelli Riccardo , Fiori Barbara , d'Inzeo Tiziana , Corbo Giuseppe Maria , Valente Salvatore , Sanguinetti Maurizio , Spanu Teresa
Published: January 2014

Spontaneous chylothorax is rare in adults. We present an unusual case that was complicated by
Prevotella bivia
empyema. Full recovery was achieved with chest tube drainage and prompt treatment with intravenous clindamycin.
A Molecular Surveillance Reveals the Prevalence of Vibrio cholerae O139 Isolates in China from 1993 to 2012
Authors: Zhang Ping , Zhou Haijian , Diao Baowei , Li Fengjuan , Du Pengcheng , Li Jie , Kan Biao , Morris J. Glenn , Wang Duochun
Published: January 2014

Vibrio cholerae
serogroup O139 was first identified in 1992 in India and Bangladesh, in association with major epidemics of cholera in both countries; cases were noted shortly thereafter in China. We characterized 211
V. cholerae
O139 isolates that were isolated at multiple sites in China between 1993 and 2012 from patients (
n
= 92) and the environment (
n
= 119). Among clinical isolates, 88 (95.7%) of 92 were toxigenic, compared with 47 (39.5%) of 119 environmental isolates. Toxigenic isolates carried the El Tor CTX prophage and toxin-coregulated pilus A gene (
tcpA
), as well as the
Vibrio
seventh pandemic island I (VSP-I) and VSP-II. Among a subset of 42 toxigenic isolates screened by multilocus sequence typing (MLST), all were in the same sequence type as a clinical isolate (MO45) from the original Indian outbreak. Nontoxigenic isolates, in contrast, generally lacked VSP-I and -II, and fell within13 additional sequence types in two clonal complexes distinct from the toxigenic isolates. In further pulsed-field gel electrophoresis (PFGE) (with NotI digestion) studies, toxigenic isolates formed 60 pulsotypes clustered in one group, while the nontoxigenic isolates formed 43 pulsotypes which clustered into 3 different groups. Our data suggest that toxigenic O139 isolates from widely divergent geographic locations, while showing some diversity, have maintained a relatively tight clonal structure across a 20-year time span. Nontoxigenic isolates, in contrast, exhibited greater diversity, with multiple clonal lineages, than did their toxigenic counterparts.
Serodiagnosis Using Microagglutination Assay during the Food-Poisoning Outbreak in Japan Caused by Consumption of Raw Beef Contaminated with Enterohemorrhagic Escherichia coli O111 and O157
Authors: Isobe Junko , Shima Tomoko , Kanatani Jun-ichi , Kimata Keiko , Shimizu Miwako , Kobayashi Naoto , Tanaka Tomoko , Iyoda Sunao , Ohnishi Makoto , Sata Tetsutaro , Watahiki Masanori
Published: January 2014

A microagglutination (MA) assay to identify antibodies to
Escherichia coli
O111 and O157 was conducted in sera collected from 60 patients during a food-poisoning outbreak affecting 181 patients in Japan which was caused by the consumption of contaminated raw beef. Enterohemorrhagic
E. coli
(EHEC) O111:H8 and/or O157:H7 was isolated from the stools of some of the patients, but the total rate of positivity for antibodies to O111 (45/60, 75.0%) was significantly higher than that for antibodies to O157 (10/60, 16.7%). The MA titers of antibodies to O111 measured in patients with hemolytic-uremic syndrome and bloody diarrhea were higher than those measured in patients with only diarrhea. In patients from whose stool no isolates of
E. coli
O111 and O157 were obtained, the positive antibody detection rates were 12/19 (63.2%) for O111 and 2/19 (10.5%) for O157, and the MA titers of antibodies to O111 measured were higher than those to O157. Similarly, the MA titers of antibodies to O111 were significantly higher than those to O157, regardless of the other groups, including groups O111, O111 and O157, and O157. These serodiagnosis results suggest that EHEC O111:H8
stx
2
played a primary role in the pathogenesis of this outbreak. Furthermore, our findings suggest that the isolates from the patients' stool specimens were not always the major causative pathogen in patients with multiple EHEC infections, because the sera from patients from whose stools only O157 was isolated were positive for antibodies to O111. Measuring antibodies to
E. coli
O antigen is helpful especially in cases with multiple EHEC infections, even with a non-O157 serotype.
Novel Vaccine Regimen Elicits Strong Airway Immune Responses and Control of Respiratory Syncytial Virus in Nonhuman Primates
Authors: Grunwald Thomas , Tenbusch Matthias , Schulte Reiner , Raue Katharina , Wolf Hans , Hannaman Drew , de Swart Rik L. , Überla Klaus , Stahl-Hennig Christiane
Published: January 2014

Induction of long-lasting immunity against viral respiratory tract infections remains an elusive goal. Using a nonhuman primate model of human respiratory syncytial virus (hRSV) infection, we compared mucosal and systemic immune responses induced by different DNA delivery approaches to a novel parenteral DNA prime-tonsillar adenoviral vector booster immunization regimen. Intramuscular (i.m.) electroporation (EP) of a DNA vaccine encoding the fusion protein of hRSV induced stronger systemic immune responses than intradermal EP, tattoo immunization, and conventional i.m. DNA injection. A single EP i.m., followed by two atraumatic tonsillar immunizations with the adenoviral vector, elicited strong systemic immune responses, an unique persistent CD4
+
and CD8
+
T cell response in the lower respiratory tract and protection from intranasal hRSV challenge. Thus, parenteral DNA priming followed by booster immunization targeted to a mucosal inductive site constitutes an effective vaccine regimen for eliciting protective immune responses at mucosal effector sites.

IMPORTANCE
The human respiratory syncytial virus (hRSV) is the most common cause of severe respiratory tract disease in infancy and leads to substantial morbidity and morality in the elderly. In this study, we compared the immunogenicity and efficacy of several gene-based immunization protocols in rhesus macaques. Thereby, we found that the combination of an initially parenterally delivered DNA vaccine with a subsequent atraumatic tonsillar adenoviral vector immunization results in a strong systemic immune response accompanied by an exceptional high T-cell response in the mucosa. Strikingly, these animals were protected against a RSV challenge infection controlling the viral replication indicated by a 1,000-fold-lower viral load in the lower respiratory tract. Since mucosal cellular responses of this strength had not been described in earlier RSV vaccine studies, this heterologous DNA prime-tonsillar boost vaccine strategy is very promising and should be pursued for further preclinical and clinical testing.
Blocking of Exchange Proteins Directly Activated by cAMP Leads to Reduced Replication of Middle East Respiratory Syndrome Coronavirus
Authors: Tao Xinrong , Mei Feng , Agrawal Anurodh , Peters Clarence J. , Ksiazek Thomas G. , Cheng Xiaodong , Tseng Chien-Te K.
Published: January 2014

The outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) infections and diseases represents a potential threat for worldwide spread and requires development of effective therapeutic strategies. In this study, we revealed a novel positive function of an exchange protein directly activated by cyclic AMP 1 (cAMP-1; Epac-1) on MERS-CoV replication. Specifically, we have shown that Epac-specific inhibitor treatment or silencing Epac-1 gene expression rendered cells resistant to viral infection. We believe Epac-1 inhibitors deserve further study as potential therapeutic agents for MERS-CoV infection.
Fifteen to Twenty Percent of HIV Substitution Mutations Are Associated with Recombination
Authors: Schlub Timothy E. , Grimm Andrew J. , Smyth Redmond P. , Cromer Deborah , Chopra Abha , Mallal Simon , Venturi Vanessa , Waugh Caryll , Mak Johnson , Davenport Miles P.
Published: January 2014

HIV undergoes high rates of mutation and recombination during reverse transcription, but it is not known whether these events occur independently or are linked mechanistically. Here we used a system of silent marker mutations in HIV and a single round of infection in primary T lymphocytes combined with a high-throughput sequencing and mathematical modeling approach to directly estimate the viral recombination and mutation rates. From >7 million nucleotides (nt) of sequences from HIV infection, we observed 4,801 recombination events and 859 substitution mutations (≈1.51 and 0.12 events per 1,000 nt, respectively). We used experimental controls to account for PCR-induced and transfection-induced recombination and sequencing error. We found that the single-cycle virus-induced mutation rate is 4.6 × 10−5mutations per nt after correction. By sorting of our data into recombined and nonrecombined sequences, we found a significantly higher mutation rate in recombined regions (P= 0.003 by Fisher's exact test). We used a permutation approach to eliminate a number of potential confounding factors and confirm that mutation occurs around the site of recombination and is not simply colocated in the genome. By comparing mutation rates in recombined and nonrecombined regions, we found that recombination-associated mutations account for 15 to 20% of all mutations occurring during reverse transcription.
Biochemical and Biological Studies of Mouse APOBEC3
Authors: Nair Smita , Sanchez-Martinez Silvia , Ji Xinhua , Rein Alan
Published: January 2014

Many murine leukemia viruses (MLVs) are partially resistant to restriction by mouse APOBEC3 (mA3) and essentially fully resistant to induction of G-to-A mutations by mA3. In contrast, Vif-deficient HIV-1 (ΔVif HIV-1) is profoundly restricted by mA3, and the restriction includes high levels of G-to-A mutation. Human APOBEC3G (hA3G), unlike mA3, is fully active against MLVs. We produced a glutathione
S
-transferase–mA3 fusion protein in insect cells and demonstrated that it possesses cytidine deaminase activity, as expected. This activity is localized within the N-terminal domain of this 2-domain protein; the C-terminal domain is enzymatically inactive but required for mA3 encapsidation into retrovirus particles. We found that a specific arginine residue and several aromatic residues, as well as the zinc-coordinating cysteines in the C-terminal domain, are necessary for mA3 packaging; a structural model of this domain suggests that these residues line a potential nucleic acid-binding interface. Mutation of a few potential phosphorylation sites in mA3 drastically reduces its antiviral activity by impairing either deaminase activity or its encapsidation. mA3 deaminates short single-stranded DNA oligonucleotides preferentially toward their 3′ ends, whereas hA3G exhibits the opposite polarity. However, when packaged into infectious ΔVif HIV-1 virions, both mA3 and hA3G preferentially induce deaminations toward the 5′ end of minus-strand viral DNA, presumably because of the sequence of events during reverse transcription
in vivo
. Despite the fact that mA3 in MLV particles does not induce detectable deaminations upon infection, its deaminase activity is easily detected in virus lysates. We still do not understand how MLV resists mA3-induced G-to-A mutation.

IMPORTANCE
One way that mammalian cells defend themselves against infection by retroviruses is with APOBEC3 proteins. These proteins convert cytidine bases to uridine bases in retroviral DNA. However, mouse APOBEC3 protein blocks infection by murine leukemia viruses without catalyzing this base change, and the mechanism of inhibition is not understood in this case. We have produced recombinant mouse APOBEC3 protein for the first time and characterized it here in a number of ways. Our mutational studies shed light on the mechanism by which mouse APOBEC3 protein is incorporated into retrovirus particles. While mouse APOBEC3 does not catalyze base changes in murine leukemia virus DNA, it can be recovered from these virus particles in enzymatically active form; it is still not clear why it fails to induce base changes when these viruses infect new cells.
Analysis of the Cullin Binding Sites of the E4orf6 Proteins of Human Adenovirus E3 Ubiquitin Ligases
Authors: Gilson Timra , Cheng Chi Ying , Hur Woosuk Steve , Blanchette Paola , Branton Philip E.
Published: January 2014

E4orf6 proteins of human adenoviruses form Cullin-based E3 ubiquitin ligase complexes that degrade cellular proteins, which impedes efficient viral replication. These complexes also include the viral E1B55K product, which is believed to recruit most substrates for ubiquitination. Heterogeneity in the composition of these ligases exists, as serotypes representing some species form Cul5-based complexes (species B2, C, D, and E), whereas others utilize Cul2 (species A and F). Adenovirus type 16 (Ad16; species B1) binds significant levels of both. In this report, we show that the Cul2 binding sequence in E4orf6 of Ad12 (species A) and Ad40 (species F) resembles the cellular consensus Cul2 box. Mutation within this Cul2 box prevents binding not only of Cul2 but also in some cases Elongin C and reduces the ability to degrade target proteins, such as Mre11 and p53. A comparable Cul2 box is not present in E4orf6 of Ad5 and other serotypes that bind Cul5; however, creation of this Cul2 box sequence in Ad5 E4orf6 promoted binding to Cul2 and Cul2-dependent degradation of Mre11. E4orf6 of Ad16 also binds Cul2; however, unlike Ad40, it does not contain an Ad12-like Cul2 box, suggesting that Ad16 binds Cul2 in a unique but perhaps nonfunctional manner, as only Cul5 binding complexes appeared able to degrade Mre11. Our extensive analyses have thus far failed to identify a consensus Cul5 binding sequence, suggesting that association occurs via a novel and perhaps complex pattern of protein-protein interactions. Nevertheless, the identification of the Cul2 box may allow prediction of Cullin specificity for all E4orf6-containing
Adenoviridae
.

IMPORTANCE
The work described in this paper is a continuation of our in-depth studies on the Cullin-based E3 ligase complexes formed by the viral E4orf6 and E1B55K proteins of all human adenoviruses. This complex induces the degradation of a growing series of cellular proteins that impede efficient viral replication. Some human adenovirus species utilize Cul5, whereas others bind Cul2. In this paper, we are the first to identify the E4orf6 Cul2 binding site, which conforms in sequence to a classic cellular Cul2 box. Ours is the first detailed biochemical and genetic analysis of a Cul2-based adenovirus ligase and provides insights into both the cooperative interactions in forming Cullin-based ligases as well as the universality of formation of all adenovirus ligase complexes. Our work now permits future analysis of the evolutionary significance of the ligase complex, work that is currently in progress in our lab.
Deciphering the Role of the Gag-Pol Ribosomal Frameshift Signal in HIV-1 RNA Genome Packaging
Authors: Nikolaitchik Olga A. , Hu Wei-Shau
Published: January 2014

A key step of retroviral replication is packaging of the viral RNA genome during virus assembly. Specific packaging is mediated by interactions between the viral protein Gag and elements in the viral RNA genome. In HIV-1, similar to most retroviruses, the packaging signal is located within the 5′ untranslated region and extends into the
gag
-coding region. A recent study reported that a region including the Gag-Pol ribosomal frameshift signal plays an important role in HIV-1 RNA packaging; deletions or mutations that affect the RNA structure of this signal lead to drastic decreases (10- to 50-fold) in viral RNA packaging and virus titer. We examined here the role of the ribosomal frameshift signal in HIV-1 RNA packaging by studying the RNA packaging and virus titer in the context of proviruses. Three mutants with altered ribosomal frameshift signal, either through direct deletion of the signal, mutation of the 6U slippery sequence, or alterations of the secondary structure were examined. We found that RNAs from all three mutants were packaged efficiently, and they generate titers similar to that of a virus containing the wild-type ribosomal frameshift signal. We conclude that although the ribosomal frameshift signal plays an important role in regulating the replication cycle, this RNA element is not directly involved in regulating RNA encapsidation.

IMPORTANCE
To generate infectious viruses, HIV-1 must package viral RNA genome during virus assembly. The specific HIV-1 genome packaging is mediated by interactions between the structural protein Gag and elements near the 5′ end of the viral RNA known as packaging signal. In this study, we examined whether the Gag-Pol ribosomal frameshift signal is important for HIV-1 RNA packaging as recently reported. Our results demonstrated that when Gag/Gag-Pol is supplied in
trans
, none of the tested ribosomal frameshift signal mutants has defects in RNA packaging or virus titer. These studies provide important information on how HIV-1 regulates its genome packaging and generate infectious viruses necessary for transmission to new hosts.
The association between body composition and toxicities from the combination of Doxil and trabectedin in patients with advanced relapsed ovarian cancer
Authors: Prado Carla M.M. , Baracos Vickie E. , Xiao Jingjie , Birdsell Laura , Stuyckens Kim , Park Youn Choi , Parekh Trilok , Sawyer Michael B.
Published: January 2014

Emerging research suggests that body composition can predict toxicity of certain chemotherapeutic agents. We used data from a clinical study to investigate associations between body composition and combined DOXIL (pegylated liposomal doxorubicin; PLD) and trabectedin (Yondelis) treatment, an effective treatment for ovarian cancer that shows high interpatient variation in toxicity profile. Patients (n = 74) participating in a phase III randomized trial of relapsed advanced ovarian cancer receiving PLD (30 mg/m2) and trabectedin (1.1 mg/m2) were included. Muscle tissue was measured by analysis of computerized tomography images, and an extrapolation of muscle and adipose tissue to lean body mass (LBM) and fat mass (FM) were employed. Toxicity profile after cycle 1 was used and graded according to the National Cancer Institute Common Toxicity Criteria (version 3). Patients presented with a wide range of body composition. In overweight and obese patients (body mass index (BMI) ≥ 25 kg/m2, n = 48) toxicity was more prevalent in those with lower BMI (p = 0.028) and a lower FM (n = 43, p = 0.034). Although LBM alone was not predictive of toxicity, a lower FM/LBM ratio was the most powerful variable associated with toxicity (p = 0.006). A different pattern emerged among normal weight patients (n = 26) where toxicity was rare among patients with smaller BMI (<21 kg/m2). A clear association between both FM and LBM (primarily driven by FM) in explaining PLD plus trabectedin toxicity emerged, but only in individuals with excess body weight, with a lower ratio predicting higher exposure and risk for toxicity.
Proceedings from the 2013 Canadian Nutrition Society Conference on Advances in Dietary Fats and Nutrition
Authors: Holub Bruce , Mutch David M. , Pierce Grant N. , Rodriguez-Leyva Delfin , Aliani Michel , Innis Sheila , Yan William , Lamarche Benoit , Couture Patrick , Ma David W.L.
Published: January 2014

The science of lipid research continues to rapidly evolve and change. New knowledge enhances our understanding and perspectives on the role of lipids in health and nutrition. However, new knowledge also challenges currently held opinions. The following are the proceedings of the 2013 Canadian Nutrition Society Conference on the Advances in Dietary Fats and Nutrition. Content experts presented state-of-the-art information regarding our understanding of fish oil and plant-based n-3 polyunsaturated fatty acids, nutrigenomics, pediatrics, regulatory affairs, and trans fats. These important contributions aim to provide clarity on the latest advances and opinions regarding the role of different types of fats in health.
Incipient speciation in the Chihuahuan Desert shrub Berberis trifoliolata under divergent climate scenarios
Authors: Angulo D.F. , Amarilla L.D. , Sosa V.
Published: January 2014

The discovery of biotic and ecological factors that influence genetic isolation in populations contributes to our understanding of speciation, one of the most important issues in evolutionary biology. In this paper, we ask whether differences in climate preferences are influencing genetic isolation in two assemblages of populations of Berberis trifoliolata Moric., the Northeastern and the Mexican Plateau groups. Agarito, as this species is known, is a remarkable shrub in the arid regions of North America and found mostly in the Chihuahuan Desert. Ecological niche modeling and two tests of niche evolution were carried out. The Ecological Niche Modeling suggests that the potential distribution of the Northeastern group does not predict that of the Mexican Plateau group, and nor does the latter predict the former. Tests of niche evolution indicate a divergent niche between these two groups. Among the most important climate factors detected in the multivariate niche evolution test are mean annual temperature and annual precipitation. We concluded that the two lineages exemplify an incipient speciation process.
Synthesis and structures of monomeric group 14 triols and their reactivity
Authors: Pop Lucian-Cristian , Kurokawa Nobuaki , Ebata Hiroaki , Tomizawa Katsuya , Tajima Tomoyuki , Ikeda Masatoshi , Yoshioka Michikazu , Biesemans Monique , Willem Rudolph , Minoura Mao , Saito Masaichi
Published: January 2014

The first stable stannanetriol and germanetriol bearing sterically congested aryl groups were synthesized by hydrolysis of the corresponding trichloro-stannane and -germane. The stannanetriol is monomeric in solution as well as in the crystalline state, as evidenced by X-ray diffraction analysis and CP-MAS NMR spectroscopy. The stannanetriol reacted with silicone grease to afford a cagelike compound having three Sn–O–Si–O–Sn linkages in the molecule. All the group 14 triols can be converted to the corresponding trihalo compounds in good yields.
Split-flow Taylor dispersion technique for diffusivity and concentration measurements of hydrazine in aqueous solution
Authors: Choudhry Kashif I. , Svishchev Igor M. , Plugatyr Andriy
Published: January 2014

A sensitive continuous-flow monitoring method is developed for the determination of the diffusion coefficient and concentration of hydrazine in an aqueous solution. The effect of pH on the diffusion coefficient of hydrazine in water was studied at room temperature using the developed split-flow Taylor dispersion technique. The hydrazine calibration curve was linear in the range of 10−1000 ppb and the limit of quantification was 10 ppb. The results showed that the diffusion coefficient of hydrazine does not change significantly over the pH range of 4.01−8.27 but increases in alkaline media of pH greater than 8.27. This method can be used for accurate determination of hydrazine concentration in aqueous flow systems.
Density operator for describing driven damped harmonic oscillator in the diffusion-limited channel
Authors: Fan Hong-Yi , Chen Qian-Fan
Published: January 2014

In the present work, the Kraus-operator sum representation of the exact solution to the master equation describing a harmonic oscillator (driven by an external source) damping in the diffusion-limited channel is obtained by virtue of the thermo-entangled state representation and the technique of integration within an ordered product of operators. According to this solution, the initial coherent state will evolve into a displaced chaotic state that manifestly exhibits quantum decoherence.
Organic–inorganic hybrid thin films based in HfO2 nanoparticles as dielectric for flexible electronics
Authors: Ambrosio R. , Arciniega O. , Carrillo A. , Moreno M. , Heredia A. , Martinez C.
Published: January 2014

In this work the synthesis and characterization of an organic–inorganic hybrid composite film based on hafnium oxide (HfO2) and polyvinylpyrrolidone (PVP) with dielectric properties is presented. These films were prepared using the sol-gel process adjusting the chemical composition to tailor the material properties, such as the dielectric and the optical band gap. The HfO2 was obtained by the hydrolysis of hafnium chloride (HfCl4) under catalysis of ethanol and deionized water, later the PVP was subsequently added to complete the hydrolysis. Finally the films were dried at 150 °C. The structural characterization of the hybrid material showed a hafnium nanoparticle size around 100 nm into the polymer matrix. The chemical structure and the high purity of the hybrid material were corroborated by X-ray photoelectron spectroscopy measurements, which showed the bounding of HfO2–PVP. The electrical characterization demonstrated that the nanostructured materials with hafnium nanoparticles improve the dielectric constant in the films with values around k = 18.5. The optical band gap, Eo, was obtained from 4 to 5.7 eV. These characteristics in our hybrid material are very promising for flexible electronics applications with the advantage of its low temperature, thermal stability, and low cost process of deposition.
Effect of hydrogen concentration on structure and photoelectric properties of a-Si:H films modified by femtosecond laser pulses
Authors: Khenkin Mark , Emelyanov Andrey , Kazanskii Andrey , Forsh Pavel , Beresna Martynas , Gecevicius Mindaugas , Kazansky Peter
Published: January 2014

The crystallization of hydrogenated amorphous silicon films with femtosecond laser pulses is one of the promising ways to produce nanocrystalline silicon for photovoltaics. The structure of laser treated films and their hydrogen content are the most important factors for determining the photoelectric properties of materials. In this work we investigated the effect of femtosecond laser irradiation of a-Si:H films with different fluences on crystalline volume fraction, hydrogen concentration, and photoelectric properties of this material. Our results point out that hydrogen out-diffusion accompanies the crystallization process. The increase of hydrogen concentration in the initial a-Si:H films structure affects the kinetics of the crystallization process, but does not lead to a substantial increase of hydrogen concentration remaining in the film after the treatment. The deficiency of hydrogen in the films’ structure results in degradation of their photoconductivity, thus other strategies of a-Si:H laser crystallization or postprocessing should be found to obtain device-quality films using ultrafast laser processing.
Relative constraints and evolution
Authors: Ochoa Juan G. Diaz
Published: January 2014

Several mathematical models of evolving systems assume that changes in the micro-states are constrained to the search of an optimal value in a local or global objective function. However, the concept of evolution requires a continuous change in the environment and species, making difficult the definition of absolute optimal values in objective functions. In this paper, we define constraints that are not absolute but relative to local micro-states, introducing a rupture in the invariance of the phase space of the system. This conceptual basis is useful to define alternative mathematical models for biological (or in general complex) evolving systems. We illustrate this concept with a modified Ising model, which can be useful to understand and model problems like the somatic evolution of cancer.
Recent techniques for PDE discretizations on polyhedral meshes
Authors: Bellomo N. , Brezzi F. , Manzini G.
Published: January 2014

This brief paper is an introduction to the papers published in a special issue devoted to survey on recent techniques for discretizing Partial Differential Equations on general polygonal and polyhedral meshes. The number of different techniques to deal with discretizations on polygonal and polyhedral meshes is quite huge, and their history is quite long. Here we concentrate on the most recent techniques, including Mimetic Finite Differences, Virtual Element Methods, and the recent developments, in this direction, of Finite Volumes and Discontinuous Galerkin Methods.
Mimetic finite differences for nonlinear and control problems
Authors: Antonietti P. F. , Beirão da Veiga L. , Bigoni N. , Verani M.
Published: January 2014

In this paper we review some recent applications of the mimetic finite difference method to nonlinear problems (variational inequalities and quasilinear elliptic equations) and optimal control problems governed by linear elliptic partial differential equations. Several numerical examples show the effectiveness of mimetic finite differences in building accurate numerical approximations. Finally, driven by a real-world industrial application (the numerical simulation of the extrusion process) we explore possible further applications of the mimetic finite difference method to nonlinear Stokes equations and shape optimization/free-boundary problems.
M-Adaptation in the mimetic finite difference method
Authors: Gyrya Vitaliy , Lipnikov Konstantin , Manzini Gianmarco , Svyatskiy Daniil
Published: January 2014

The mimetic finite difference method produces a family of schemes with equivalent properties such as the stencil size, stability region, and convergence order. Each member of this family is defined by a set of parameters which can be chosen locally for every mesh element. The number of parameters depends on the geometry of a particular mesh element. M-Adaptation is a new adaptation methodology that identifies a member of this family with additional (superior) properties compared to the other schemes in the family. We analyze the enforcement of the discrete maximum principles for the diffusion equation in the primal and dual forms, the reduction of numerical dispersion and anisotropy for the acoustic wave equation, and the optimization of the performance of multi-grid solvers.
OPTIMIZATION OF QUALITY FACTOR IN PHOTONIC CRYSTAL CAVITIES THROUGH FINITE DIFFERENCE TIME DOMAIN AND MULTIPOLE EXPANSION TECHNIQUE
Authors: MAZAHERI AZARDOKHT , HAMIDIPOUR ABOUZAR , JANNESARY REIHANEH , ZAMIRI SAEID , MOHTASHAMI ABBAS , ZARBAKHSH JAVAD
Published: January 2014

Local density of photonic states calculation based on multipole expansion method is a powerful tool for studying spontaneous emission and calculation of photon confinement in photonic crystal cavities. Using multipole expansion method, we calculate local density of states and quality factor of a two-dimensional three angle photonic crystal cavity. We also compare this quality factor result with the one calculated using finite difference time domain of a pulse response. It turns out that the local density of states calculation is more accurate and computationally less expensive. It is shown that shifting and changing the size of neighboring cylinders in the vicinity of photonic crystal cavity has a large impact on the mode volume and confinement. It is also described how the increasing of quality factor can be split up into local optimization of neighboring rods and the effect of increasing the number of photonic crystal layers, which exponentially increases the quality factor. This finding strongly suggests that the number of layers can be excluded from an optimization procedure. We also present structural design rules and geometrical freedom contour plots for the neighboring cylinders. These design rules can be used in further optimization of photonic crystal cavities.
THE AMPLITUDE AND PHASE MEASUREMENTS OF FEMTOSECOND PULSE USING FRINGE FREE INTERFEROMETRY OF SPECTRAL HIGH-RESOLUTION METHOD
Authors: LEI LIANG , WEI YUAN , ZHOU JIN-YUN , WANG BO , WANG QU , XING XIAO-BO
Published: January 2014

In this paper, we present analytical and experimental results of a novel method which enables significant simplifications in spectral shearing interferometry as applied for ultrashort optical pulse measurements. The method attempts to improve the superiority in conventional spectral phase interferometry for direct electric-field reconstruction (SPIDER). It does not split a test pulse into two parts, but compensate for the delay time between two quasi-monochromatic frequency components in a chirped pulse with spectral and temporal shear to produce an interferogram without fringe. Fringe free interferogram could simplify data processing procedure and reduce the restriction on resolution of spectrometer. The experimental setup avoids the influence of material dispersion with real-time and single-shot nature, and could be made up as a miniaturization measurement device. Although being short of the beauties in SPIDER, it still could be an optional femtosecond pulse measurement method in certain condition.
Functional and Symbolic Values of Cloud Terminals: A Study of User Acceptance and Purchasing Behaviors
Authors: Pan Yu , Luo Lijuan , Liu Dan , Gao Li , Rao Hengyi
Published: January 2014

The purchasing behavior of cloud terminals is increasingly shaped by the emerging cloud services. Rather than its hardware configuration, performance of cloud intelligent terminals such as the Chromebook is more and more dependent on the cloud service capability. However, it remains unknown what factors will drive user's acceptance and purchase of these cloud terminals. Using the Chromebook and MacBook as two representative products, this study models user's acceptance and purchasing behavior of cloud terminals and examines multiple factors driving the consumer's purchasing decision from the perspective of functional and symbolic values. The results emphasize the importance of symbolic values and cost, and propose that symbolic values of different cloud terminals have different effects on consumers' acceptance and purchase. It has important implications for companies to design and sell cloud terminals based on user's acceptance and purchase intentions.
Role of arginine 209 in the conformational transition of the protein kinase A regulatory subunit RIα A-domain
Authors: Rogacheva Olga N. , Stefanov Vasiliy E. , Shchegolev Boris F. , Vershinina Elena A. , Savvateeva-Popova Elena V.
Published: January 2014

Using the combination of molecular dynamics (MD) simulations and geometric clustering we analyzed the role of arginine at 209 position in the transition of protein kinase A Iα (PKA Iα) regulatory subunit A-domain from H- to B-conformation and stabilization of the latter. The mechanism underlying the role of the residue at position 209 in the realization of B-conformation includes: (1) possibility to bind the ligand tightly (if transition happens in the presence of cAMP), (2) capability to hold β2β3-loop in the correct conformation, (3) tendency of residue at 209 position to stabilize B-conformation in the absence and in presence of the ligand. In terms of the effect produced on transition of A-domain from H- to B-conformation in the presence of cAMP, mutational substitutions for R209 can be arranged in the following order: Glu(Gly)>Lys>Ile. In the absence of cAMP the order is different Lys>Gly>Glu>Ile. Thus, our results allow us to presume that the role of arginine at 209 position can be important though not crucial.
WELL-POSEDNESS OF THE CAUCHY PROBLEM FOR THE CHERN–SIMONS–DIRAC SYSTEM IN TWO DIMENSIONS
Authors: OKAMOTO MAMORU
Published: January 2014

We consider the Cauchy problem associated with the Chern–Simons–Dirac system in ℝ1+2. Using gauge invariance, we reduce the Chern–Simons–Dirac system to a Dirac equation and we uncover the null structure of this Dirac equation. Next, relying on null structure estimates, we establish that the Cauchy problem associated with this Dirac equation is locally-in-time well-posed in the Sobolev space Hsfor all s > 1/4. Our proof uses modified L4-type estimates.
PRIORITY-BASED TASK REASSIGNMENTS IN HIERARCHICAL 2D MESH-CONNECTED SYSTEMS USING TABLEAUX
Authors: KIM DOHAN
Published: January 2014

Task reassignments in two-dimensional (2D) mesh-connected systems (2D-MSs) have been researched for several decades. We propose a hierarchical 2D mesh-connected system (2D-HMS) in order to exploit the regular nature of a 2D-MS. In our approach priority-based task assignments and reassignments in a 2D-HMS are represented by tableaux and their algorithms. We show how task relocations for a priority-based task reassignment in a 2D-HMS are reduced to a jeu de taquin slide.