bluuebunny/crossref_metadata_2025 huggingface dataset:
Validation of the Gen-Probe Aptima Qualitative HIV-1 RNA Assay for Diagnosis of Human Immunodeficiency Virus Infection in Infants
Authors: Fiscus Susan A. , McMillion Takesha , Nelson Julie A. E. , Miller William C.
Published: October 2013

The qualitative Roche HIV-1 DNA Amplicor assay has been used for the past 20 years to diagnose HIV infection in infants and young children but is being phased out; hence, alternative assays must be found. The Gen-Probe Aptima qualitative HIV-1 RNA assay is currently the only FDA-cleared HIV-1 nucleic acid assay approved for diagnosis, but data on the use of this assay with infant plasma are limited. We assessed Aptima's performance using control material for reproducibility and limit of detection and 394 plasma samples (0.2 to 0.5 ml) from HIV-exposed infected and uninfected infants and children for analytical sensitivity and specificity. Assays to assess within-run repeatability and between-run reproducibility indicated that the controls with 10,000 (5 of 5), 200 (5 of 5), 100 (16 of 16), 50 (12 of 12), and 25 (20 of 20) HIV-1 RNA copies/ml (cp/ml) were always positive, and negatives were always negative (20 of 20). The limit of detection was 14 cp/ml, as determined by probit analysis. The analytic sensitivity of the assay was 99.5% (189/190 samples; 95% confidence interval [CI], 97.1 to 99.9%) and specificity was 99.5% (199/200 samples; 95% CI, 97.2 to 99.9%). These results suggest that the assay is suitable for early infant diagnosis of HIV-1.
Impact of the New Abbott
m
PLUS Feature on Clinical Laboratory Efficiencies of Abbott RealTi
m
e Assays for Detection of HIV-1, Hepatitis C Virus, Hepatitis B Virus, Chlamydia trachomatis, and Neisseria gonorrhoeae
Authors: Lucic Danijela , Jones Sara , Wiesneth Russ , Barry Cathy , Webb Erika , Belova Larissa , Dolan Peggy , Ho Shiaolan , Abravaya Klara , Cloherty Gavin
Published: October 2013

Diagnostic laboratories are under increasing pressure to improve and expand their services. Greater flexibility in sample processing is a critical factor that can improve the time to results while reducing reagent waste, making laboratories more efficient and cost-effective. The introduction of the Abbott
m
PLUS feature, with the capacity for extended use of amplification reagents, significantly increases the flexibility of the
m
2000 platform and enables laboratories to customize their workflows based on sample arrival patterns. The flexibility in sample batch size offered by
m
PLUS enables significant reductions in processing times. For hepatitis B virus tests, a reduction in sample turnaround times of up to 30% (105 min) was observed for batches of 12 samples compared with those for batches of 24 samples; for
Chlamydia trachomatis
/
Neisseria gonorrhoeae
tests, the ability to run batches of 24 samples reduced the turnaround time by 83% (54 min) compared with that for batches of 48 samples. Excellent correlations between
m
PLUS and
m
2000 standard condition results were observed for all RealTi
m
e viral load assays evaluated in this study, with correlation
r
values of 0.998 for all assays tested. For the qualitative RealTi
m
e
C. trachomatis
/
N. gonorrhoeae
assay, the overall agreements between the two conditions tested were >98% for
C. trachomatis
and 100% for
N. gonorrhoeae
. Comparable precision results were observed for the two conditions tested for all RealTi
m
e assays. The enhanced
m
PLUS capability provides clinical laboratories with increased efficiencies to meet increasingly stringent turnaround time requirements without increased costs associated with discarding partially used amplification reagents.
Comparison of Next-Generation Sequencing and Clone-Based Sequencing in Analysis of Hepatitis B Virus Reverse Transcriptase Quasispecies Heterogeneity
Authors: Gong Ling , Han Yue , Chen Li , Liu Feng , Hao Pei , Sheng Jia , Li Xin-Hua , Yu De-Min , Gong Qi-Ming , Tian Fei , Guo Xiao-kui , Zhang Xin-Xin
Published: October 2013

We previously reported that, based on clone-based sequencing (CBS), hepatitis B virus (HBV) heterogeneity within the reverse transcriptase (RT) region was a predictor of antiviral efficacy. Here, by comparing ultradeep pyrosequencing (UDPS), i.e., next-generation sequencing (NGS), with CBS in characterizing the genetic heterogeneity of HBV quasispecies within the RT region, we evaluated the performance of UDPS in the analysis of HBV viral populations. HBV genomic DNA was extracted from serum samples from 31 antiviral treatment-naive patients with chronic hepatitis B. The RT region quasispecies were analyzed in parallel using CBS and UDPS. Characterization of quasispecies heterogeneity was conducted using bioinformatics analysis. Quasispecies complexity values were calculated with the formula
Sn
= −Σ

i

(

p
i

ln

p
i

)/ln
N
. The number of qualified strains obtained by UDPS was much larger than that obtained by CBS (
P
< 0.001). Pearson analysis showed that there was a positive correlation of quasispecies complexity values at the nucleotide level for the two methods (
P
< 0.05), while the complexity value derived from UDPS data was higher than that derived from CBS data (
P
< 0.001). Study of the prevalences of variations within the RT region showed that CBS detected an average of 9.7 ± 1.1 amino acid substitutions/sample and UDPS detected an average of 16.2 ± 1.4 amino acid substitutions/sample. The phylogenetic analysis based on UDPS data showed more genetic entities than did that based on CBS data. Viral heterogeneity determination by the UDPS technique is more sensitive and efficient in terms of low-abundance variation detection and quasispecies simulation than that by the CBS method, although imperfect, and thus sheds light on the future clinical application of NGS in HBV quasispecies studies.
Presence of Cross-Reactions with Other Viral Encephalitides in the Indirect Fluorescent-Antibody Test for Diagnosis of Rabies
Authors: Rudd Robert J. , Appler Kim A. , Wong Susan J.
Published: October 2013

The antemortem diagnosis of rabies in humans employs techniques that require accuracy, speed, and sensitivity. A combination of histochemical analysis,
in vitro
virus isolation, immunological methods, and molecular amplification procedures are utilized in efforts to diagnose the disease. Modern medicine now offers potentially life-saving treatment for a disease that was considered invariably fatal once clinical signs develop. However, medical intervention efforts require a rapid and accurate diagnosis as early in the course of clinical disease as possible. Indirect fluorescent-antibody (IFA) testing on cerebrospinal fluid and serum specimens provides rapid results, but the specificity of the assay has not been well studied. Because false-positive IFA results could significantly affect patient treatment and outcomes, it is critical to understand the specificity of this assay. In this study, IFA testing was performed on 135 cerebrospinal fluid and serum specimens taken from patients with viral encephalitis or a presumed viral infection involving an agent other than rabies virus. Results indicate that false-positive results can occur in interpreting the rabies IFA test. Staining patterns morphologically similar to antirabies staining were observed in 7 of the 135 cerebrospinal fluid specimens examined. In addition, a majority of the cerebrospinal fluid specimens tested from patients with encephalitis presented immunoglobulin that bound to antigens present in the cell culture substrate. Of marked concern was the frequent presence of cross-reactive antibodies in encephalitis cases associated with West Nile and Powassan flaviviruses. Because IFA testing for rabies on human specimens may result in false-positive results, it should not be used as the sole basis for initiating antirabies treatment.
Marseillevirus Adenitis in an 11-Month-Old Child
Authors: Popgeorgiev Nikolay , Michel Gerard , Lepidi Hubert , Raoult Didier , Desnues Christelle
Published: October 2013

A Marseillevirus (giant virus of amoeba) has been found in the blood and stool samples of individuals who otherwise appear to be healthy. During an attempt to define a serological cutoff for Marseillevirus by enzyme-linked immunosorbent assay (ELISA) in children, we serendipitously detected high antibody responses to Marseillevirus in an 11-month-old boy suffering from adenitis. Marseillevirus DNA was then found in his blood using PCR and with a unique sequence. We identified Marseillevirus in a lymph node using fluorescence
in situ
hybridization (FISH) and immunohistochemistry, and the lymph node was removed surgically. The child was declared to be cured 1 year later. We conclude that adenitis during early childhood may be caused by Marseillevirus.
wzi
Gene Sequencing, a Rapid Method for Determination of Capsular Type for Klebsiella Strains
Authors: Brisse Sylvain , Passet Virginie , Haugaard Anita Björk , Babosan Anamaria , Kassis-Chikhani Najiby , Struve Carsten , Decré Dominique
Published: October 2013

Pathogens of the genus
Klebsiella
have been classified into distinct capsular (K) types for nearly a century. K typing of
Klebsiella
species still has important applications in epidemiology and clinical microbiology, but the serological method has strong practical limitations. Our objective was to evaluate the sequencing of
wzi
, a gene conserved in all capsular types of
Klebsiella pneumoniae
that codes for an outer membrane protein involved in capsule attachment to the cell surface, as a simple and rapid method for the prediction of K type. The sequencing of a 447-nucleotide region of
wzi
distinguished the K-type reference strains with only nine exceptions. A reference
wzi
sequence database was created by the inclusion of multiple strains representing K types associated with high virulence and multidrug resistance. A collection of 119 prospective clinical isolates of
K. pneumoniae
were then analyzed in parallel by
wzi
sequencing and classical K typing. Whereas K typing achieved typeability for 81% and discrimination for 94.4% of the isolates, these figures were 98.1% and 98.3%, respectively, for
wzi
sequencing. The prediction of K type once the
wzi
allele was known was 94%.
wzi
sequencing is a rapid and simple method for the determination of the K types of most
K. pneumoniae
clinical isolates.
Large Oligoclonal Outbreak Due to Klebsiella pneumoniae ST14 and ST26 Producing the FOX-7 AmpC β-Lactamase in a Neonatal Intensive Care Unit
Authors: Arena Fabio , Giani Tommaso , Becucci Elisa , Conte Viola , Zanelli Giacomo , D'Andrea Marco Maria , Buonocore Giuseppe , Bagnoli Franco , Zanchi Alessandra , Montagnani Francesca , Rossolini Gian Maria
Published: October 2013

A large outbreak caused by expanded-spectrum cephalosporin-resistant
Klebsiella pneumoniae
(ESCRKP) was observed in a neonatal intensive care unit (NICU) in central Italy. The outbreak involved 127 neonates (99 colonizations and 28 infections, with seven cases of sepsis and two deaths) over a period of more than 2 years (February 2008 to April 2010). Characterization of the 92 nonredundant isolates that were available for further investigation revealed that all of them except one produced the FOX-7 AmpC-type β-lactamase and belonged to either sequence type 14 (ST14) or ST26. All of the FOX-7-positive isolates were resistant to cefotaxime, ceftazidime, and piperacillin-tazobactam, while 76% were susceptible to cefepime, 98% to ertapenem, 99% to meropenem, and 100% to imipenem. The two carbapenem-nonsusceptible isolates had alterations in the genes encoding outer membrane proteins K35 and K36, which resulted in truncated and likely nonfunctional proteins. The outbreak was eventually controlled by the reinforcement of infection control measures based on a multitiered interventional approach. This is the first report of a large NICU outbreak caused by ESCRKP producing an AmpC-type enzyme. This study demonstrates that AmpC-type enzyme-producing strains can cause large outbreaks with significant morbidity and mortality effects (the mortality rate at 14 days was 28.5% for episodes of sepsis), and it underscores the role of laboratory-based surveillance and infection control measures to contain similar episodes.
Clinical Prediction and Diagnosis of Neurosyphilis in HIV-Infected Patients with Early Syphilis
Authors: Dumaresq Jeannot , Langevin Stéphanie , Gagnon Simon , Serhir Bouchra , Deligne Benoît , Tremblay Cécile , Tsang Raymond S. W. , Fortin Claude , Coutlée François , Roger Michel
Published: October 2013

The diagnosis of neurosyphilis (NS) is a challenge, especially in HIV-infected patients, and the criteria for deciding when to perform a lumbar puncture (LP) in HIV-infected patients with syphilis are controversial. We retrospectively reviewed demographic, clinical, and laboratory data from 122 cases of HIV-infected patients with documented early syphilis who underwent an LP to rule out NS, and we evaluated 3 laboratory-developed validated real-time PCR assays, the
Treponema pallidum
particle agglutination (TPPA) assay, the fluorescent treponemal antibody absorption (FTA-ABS) assay, and the line immunoassay INNO-LIA Syphilis, for the diagnosis of NS from cerebrospinal fluid (CSF) samples of these patients. NS was defined by a reactive CSF-VDRL test result and/or a CSF white blood cell (WBC) count of >20 cells/μl. Thirty of the 122 patients (24.6%) had early NS. Headache, visual symptoms, a CD4 cell count of <500 cells/μl, and viremia, as defined by an HIV-1 RNA count of ≥50 copies/ml, were associated with NS in multivariate analysis (
P
= <0.001 for each factor). Blood serum rapid plasma reagin (RPR) titers were not associated with early NS (
P
= 0.575). For the diagnosis of NS, the PCR, FTA-ABS, TPPA, and INNO-LIA assays had sensitivities of 58%, 100%, 68%, and 100%, specificities of 67%, 12%, 49%, and 13%, and negative predictive values of 85%, 100%, 84%, and 100%, respectively. Visual disturbances, headache, uncontrolled HIV-1 viremia, and a CD4 cell count of <500 cells/μl were predictors of NS in HIV-infected patients with early syphilis, while blood serum RPR titers were not; therefore, RPR titers should not be used as the sole criterion for deciding whether to perform an LP in early syphilis. When applied to CSF samples, the INNO-LIA Syphilis assay easily helped rule out NS.
The μ1 72-96 Loop Controls Conformational Transitions during Reovirus Cell Entry
Authors: Sarkar Payel , Danthi Pranav
Published: October 2013

The reovirus outer capsid protein μ1 forms a lattice surrounding the viral core. In the native state, μ1 determines the environmental stability of the viral capsid. Additionally, during cell entry, μ1 undergoes structural rearrangements that facilitate delivery of the viral cores across the membrane. To determine how the capsid-stabilizing functions of μ1 impinge on the capacity of μ1 to undergo conformational changes required for cell entry, we characterized viruses with mutations engineered at charged residues within the μ1 loop formed by residues 72 to 96 (72-96 loop). This loop is proposed to stabilize the capsid by mediating interactions between neighboring μ1 trimers and between trimers and the core. We found that mutations at Glu89 (E89) within this loop produced viruses with compromised efficiency for completing their replication cycle. ISVPs of E89 mutants converted to ISVP*s more readily than those of wild-type viruses. The E89 mutants yielded revertants with second-site substitutions within regions that mediate interaction between μ1 trimers at a site distinct from the 72-96 loop. These viruses also contained changes in regions that control interactions within μ1 trimers. Viruses containing these second-site changes displayed restored plaque phenotypes and were capable of undergoing ISVP-to-ISVP* conversion in a regulated manner. These findings highlight regions of μ1 that stabilize the reovirus capsid and demonstrate that an enhanced propensity to form ISVP*s in an unregulated manner compromises viral fitness.
Hepatitis B Virus Inhibits Apoptosis of Hepatoma Cells by Sponging the MicroRNA 15a/16 Cluster
Authors: Liu Ningning , Zhang Jinfang , Jiao Tong , Li Zhiwei , Peng Jirun , Cui Zhuqingqing , Ye Xin
Published: October 2013

Hepatitis B virus (HBV) causes chronic hepatitis in hundreds of millions of people worldwide, which can eventually lead to hepatocellular carcinoma (HCC). The molecular mechanisms underlying HBV persistence are not well understood. In this study, we found that HBV inhibited the chemotherapy drug etoposide-induced apoptosis of hepatoma cells. Further analysis revealed that HBV mRNAs possess a microRNA 15a/16 (miR-15a/16)-complementary site (HBV nucleotides [nt] 1362 to 1383) that acts as a sponge to bind and sequester endogenous miR-15a/16. Consequently, Bcl-2, known as the target of miR-15a/16, was upregulated in HBV-infected cells. The data from HBV-transgenic mice further confirmed that HBV transcripts cause the reduction of miR-15a/16 and increase of Bcl-2. More importantly, we examined the levels of HBV transcripts and miR-15a/16 in HBV-infected HCC from patients and found that the amount of HBV mRNA and the level of miR-15a/16 were negatively correlated. Consistently, the level of Bcl-2 mRNA was upregulated in HBV-infected patients. In conclusion, we identified a novel HBV mRNA–miR-15a/16–Bcl-2 regulatory pathway that is involved in inhibiting etoposide-induced apoptosis of hepatoma cells, which may contribute to facilitating chronic HBV infection and hepatoma development.
Characteristics of Oncolytic Vesicular Stomatitis Virus Displaying Tumor-Targeting Ligands
Authors: Ammayappan Arun , Peng Kah-Whye , Russell Stephen J.
Published: October 2013

We sought proof of principle that tumor-targeting ligands can be displayed on the surface of vesicular stomatitis virus (VSV) by engineering its glycoprotein. Here, we successfully rescued VSVs displaying tumor vasculature-targeting ligands. By using a rational approach, we investigated various feasible insertion sites on the G protein of VSV (VSV-G) for display of tumor vasculature-targeting ligands, cyclic RGD (cRGD) and echistatin. We found seven sites on VSV-G that tolerated insertion of the 9-residue cRGD peptide, two of which could tolerate insertion of the 49-amino acid echistatin domain. All of the ligand-displaying viruses replicated as well as the parental virus.
In vitro
studies demonstrated that the VSV-echistatin viruses specifically bound to targeted integrins. Since the low-density lipoprotein receptor (LDLR) was recently identified as a major receptor for VSV, we investigated the entry of ligand-displaying viruses after masking LDLR. The experiment showed that the modified viruses can enter the cell independently of LDLR, whereas entry of unmodified virus is significantly blocked by a specific monoclonal antibody against LDLR. Both parental and ligand-displaying viruses displayed equal oncolytic efficacies in a syngeneic mouse myeloma model. We further demonstrated that single-chain antibody fragments against tumor-specific antigens can be inserted at the N terminus of the G protein and that corresponding replication-competent VSVs can be rescued efficiently. Overall, we demonstrated that functional tumor-targeting ligands can be displayed on replication-competent VSVs without perturbing viral growth and oncolytic efficacy. This study provides a rational foundation for the future development of fully retargeted oncolytic VSVs.
5-HT
2
Receptors Facilitate JC Polyomavirus Entry
Authors: Assetta Benedetta , Maginnis Melissa S. , Gracia Ahufinger Irene , Haley Sheila A. , Gee Gretchen V. , Nelson Christian D. S. , O'Hara Bethany A. , Allen Ramdial Stacy-ann A. , Atwood Walter J.
Published: October 2013

The human JC polyomavirus (JCPyV) causes the rapidly progressing demyelinating disease progressive multifocal leukoencephalopathy (PML). The disease occurs most often in individuals with AIDS but also occurs in individuals receiving immunomodulatory therapies for immune-related diseases such as multiple sclerosis. JCPyV infection of host cells requires the pentasaccharide lactoseries tetrasaccharide c (LSTc) and the serotonin receptor 5-hydroxytryptamine (5-HT) receptor 5-HT
2A
R. While LSTc is involved in the initial attachment of virus to cells via interactions with VP1, the mechanism by which 5-HT
2A
R contributes to infection is not clear. To further define the roles of serotonin receptors in infection, HEK293A cells, which are poorly permissive to JCPyV, were transfected with 14 different isoforms of serotonin receptor. Only 5-HT
2
receptors were found to support infection by JCPyV. None of the other 11 isoforms of serotonin receptor supported JCPyV infection. Expression of 5-HT
2
receptors did not increase binding of JCPyV to cells, but this was not unexpected, given that the cells uniformly expressed the major attachment receptor, LSTc. Infection of these cells remained sensitive to inhibition with soluble LSTc, confirming that LSTc recognition is required for JCPyV infection. Virus internalization into HEK293A cells was significantly and specifically enhanced when 5HT
2
receptors were expressed. Taken together, these data confirm that the carbohydrate LSTc is the attachment receptor for JCPyV and that the type 2 serotonin receptors contribute to JCPyV infection by facilitating entry.
LINE-1 Retrotransposable Element DNA Accumulates in HIV-1-Infected Cells
Authors: Jones R. Brad , Song Haihan , Xu Yang , Garrison Keith E. , Buzdin Anton A. , Anwar Naveed , Hunter Diana V. , Mujib Shariq , Mihajlovic Vesna , Martin Eric , Lee Erika , Kuciak Monika , Raposo Rui André Saraiva , Bozorgzad Ardalan , Meiklejohn Duncan A. , Ndhlovu Lishomwa C. , Nixon Douglas F. , Ostrowski Mario A.
Published: October 2013

Type 1 long-interspersed nuclear elements (L1s) are autonomous retrotransposable elements that retain the potential for activity in the human genome but are suppressed by host factors. Retrotransposition of L1s into chromosomal DNA can lead to genomic instability, whereas reverse transcription of L1 in the cytosol has the potential to activate innate immune sensors. We hypothesized that HIV-1 infection would compromise cellular control of L1 elements, resulting in the induction of retrotransposition events. Here, we show that HIV-1 infection enhances L1 retrotransposition in Jurkat cells in a Vif- and Vpr-dependent manner. In primary CD4
+
cells, HIV-1 infection results in the accumulation of L1 DNA, at least the majority of which is extrachromosomal. These data expose an unrecognized interaction between HIV-1 and endogenous retrotransposable elements, which may have implications for the innate immune response to HIV-1 infection, as well as for HIV-1-induced genomic instability and cytopathicity.
Rescue of Maturation Off-Pathway Products in the Assembly of Pseudomonas Phage ϕ6
Authors: Sun Xiaoyu , Pirttimaa Markus J. , Bamford Dennis H. , Poranen Minna M.
Published: October 2013

Many complex viruses use an assembly pathway in which their genome is packaged into an empty procapsid which subsequently matures into its final expanded form. We utilized
Pseudomonas
phage ϕ6, a well-established virus assembly model, to probe the plasticity of the procapsid maturation pathway. The ϕ6 packaging nucleoside triphosphatase (NTPase), which powers sequential translocation of the three viral genomic single-stranded RNA molecules to the procapsid during capsid maturation, is part of the mature ϕ6 virion but may spontaneously be dissociated from the procapsid shell. We demonstrate that the dissociation of NTPase subunits results in premature capsid expansion, which is detected as a change in the sedimentation velocity and as defects in RNA packaging and transcription activity. However, this dead-end conformation of the procapsids was rescued by the addition of purified NTPase hexamers, which efficiently associated on the NTPase-deficient particles and subsequently drove their contraction to the compact naive conformation. The resulting particles regained their biological and enzymatic activities, directing them into a productive maturation pathway. These observations imply that the maturation pathways of complex viruses may contain reversible steps that allow the rescue of the off-pathway conformation in an overall unidirectional virion assembly pathway. Furthermore, we provide direct experimental evidence that particles which have different physical properties (distinct sedimentation velocities and conformations) display different stages of the genome packaging program and show that the transcriptional activity of the ϕ6 procapsids correlates with the number of associated NTPase subunits.
Highly Sensitive Real-Time
In Vivo
Imaging of an Influenza Reporter Virus Reveals Dynamics of Replication and Spread
Authors: Tran Vy , Moser Lindsey A. , Poole Daniel S. , Mehle Andrew
Published: October 2013

The continual public health threat posed by the emergence of novel influenza viruses necessitates the ability to rapidly monitor infection and spread in experimental systems. To analyze real-time infection dynamics, we have created a replication-competent influenza reporter virus suitable for
in vivo
imaging. The reporter virus encodes the small and bright NanoLuc luciferase whose activity serves as an extremely sensitive readout of viral infection. This virus stably maintains the reporter construct and replicates in culture and in mice with near-native properties. Bioluminescent imaging of the reporter virus permits serial observations of viral load and dissemination in infected animals, even following clearance of a sublethal challenge. We further show that the reporter virus recapitulates known restrictions due to host range and antiviral treatment, suggesting that this technology can be applied to studying emerging influenza viruses and the impact of antiviral interventions on infections
in vivo
. These results describe a generalizable method to quickly determine the replication and pathogenicity potential of diverse influenza strains in animals.
Epstein-Barr Virus Coinfection in Children Boosts Cytomegalovirus-Induced Differentiation of Natural Killer Cells
Authors: Saghafian-Hedengren Shanie , Sohlberg Ebba , Theorell Jakob , Carvalho-Queiroz Claudia , Nagy Noémi , Persson Jan-Olov , Nilsson Caroline , Bryceson Yenan T. , Sverremark-Ekström Eva
Published: October 2013

During childhood, infections with cytomegalovirus (CMV) and Epstein-Barr virus (EBV) can occur in close temporal proximity. Active, as well as latent, CMV infection is associated with enlarged subsets of differentiated natural killer (NK) and cytotoxic T cells. How EBV infection may influence CMV-driven immune differentiation is not known. We found that EBV coinfection selectively influenced the NK cell compartment of CMV-seropositive (CMV
+
) children. Coinfected children had significantly higher proportions of peripheral-blood NKG2C
+
NK cells than CMV
+
EBV
−
children.
Ex vivo
NK cell degranulation after target cell stimulation and plasma IL-15 levels were significantly higher in CMV
+
children. EBV coinfection was related to the highest levels of plasma interleukin-15 (IL-15) and IL-12p70. Remarkably,
in vitro
EBV infection of peripheral blood mononuclear cells (PBMC) from EBV
−
CMV
+
children increased NKG2C
+
NK cell proportions. A similar tendency was seen in cocultures of PBMC with EBV
+
lymphoblastoid B-cell lines (LCL) and IL-15. After K562 challenge, NKG2C
+
NK cells excelled in regard to degranulation and production of gamma interferon, regardless of whether there was previous coculture with LCL. Taken together, our data suggest that dual latency with these herpesviruses during childhood could contribute to an
in vivo
environment supporting differentiation and maintenance of distinct NK cell populations. This viral imprint may affect subsequent immune responses through altered distributions of effector cells.
Alpha Interferon Restricts Human T-Lymphotropic Virus Type 1 and 2
De Novo
Infection through PKR Activation
Authors: Cachat Anne , Chevalier Sébastien Alain , Alais Sandrine , Ko Nga Ling , Ratner Lee , Journo Chloé , Dutartre Hélène , Mahieux Renaud
Published: October 2013

Type I interferon (IFN-I) inhibits the replication of different viruses. However, the effect of IFN-I on the human T-lymphotropic virus type 1 (HTLV-1) viral cycle is controversial. Here, we investigated the consequences of IFN-α addition for different steps of HTLV-1 and HTLV-2 infection. We first show that alpha interferon (IFN-α) efficiently impairs HTLV-1 and HTLV-2
de novo
infection in a T cell line and in primary lymphocytes. Using pseudotyped viruses expressing HTLV-1 envelope, we then show that cell-free infection is insensitive to IFN-α, demonstrating that the cytokine does not affect the early stages of the viral cycle. In contrast, intracellular levels of Gag, Env, or Tax protein are affected by IFN-α treatment in T cells, primary lymphocytes, or 293T cells transfected with HTLV-1 or HTLV-2 molecular clones, demonstrating that IFN-α acts during the late stages of infection. We show that IFN-α does not affect Tax-mediated transcription and acts at a posttranscriptional level. Using either small interfering RNA (siRNA) directed against PKR or a PKR inhibitor, we demonstrate that PKR, whose expression is induced by interferon, plays a major role in IFN-α-induced HTLV-1/2 inhibition. These results indicate that IFN-α has a strong repressive effect on the HTLV-1 and HTLV-2 viral cycle during
de novo
infection of cells that are natural targets of the viruses.
Strangulated diaphragmatic hernia presenting at 7 weeks of life as intractable shock
Authors: Ismail Abdul Qader Tahir , Alake Oluwaseyi , El-Shimy Nagui
Published: October 2013

A 7-week-old infant presented to hospital pale and floppy, with 5 s capillary refill time. Blood gas showed severe acidosis (pH 6.86, partial pressure of carbondioxide 10.55 kPa, base excess 21.1). Hypotension persisted despite several fluid boluses so she was intubated and started on inotropic support. A chest X-ray revealed a congenital diaphragmatic hernia (CDH). Despite steroids and blood transfusions she remained unstable, and could not be resuscitated following cardiac arrest. Postmortem revealed 39 cm of herniated, necrotic colon. 5–25% of CDH presents after the neonatal period, and while not associated with pulmonary hypoplasia is primarily still a diaphragmatic defect. In late presenting cases, herniation occurs shortly prior to developing symptoms; therefore, an antenatal ultrasound (US) cannot pick it up. If we could diagnose the isolated diaphragmatic defect antenatally, this would allow elective postnatal surgical closure. This is not feasible currently; however, with the advent of antenatal three-dimensional US scans it may be possible in the future.
Inactivation ofBacillusspores in decontamination wash down wastewater using chlorine bleach solution
Authors: Muhammad Nur , Gallardo Vicente J. , Schupp Donald A. , Krishnan E. Radha , Minamyer K. Scott , Rice Eugene W.
Published: October 2013

Bacillus anthracis spores are highly resistant to disinfection. The effectiveness of sodium hypochlorite (bleach) solution for the inactivation of Bacillus atrophaeus subspecies globigii spores (a surrogate for Bacillus anthracis) in wash down wastewater was evaluated by a series of bench-scale and pilot-scale experiments. The wastewater was generated from a simulated decontamination of interior laboratory surfaces and personal protective equipment. A concentration of approximately 5% (v/v) bleach solution was adequate for a ≥7 log10inactivation of Bacillus spores spiked in wastewater after 10 min of contact time at room temperature. This sodium hypochlorite dose is less than the U.S. National Response Team-recommended formulation of 10% (v/v) bleach solution with 10% (v/v) vinegar. For the wash down waters evaluated, the addition of vinegar was not required. Inactivation of Bacillus spores was faster when a detergent was added to the wash down waters tested.
Spatio-temporal variability in movement, age, and growth of mountain whitefish (Prosopium williamsoni) in a river network based upon PIT tagging and otolith chemistry
Authors: Benjamin Joseph R. , Wetzel Lisa A. , Martens Kyle D. , Larsen Kimberly , Connolly Patrick J.
Published: October 2013

Connectivity of river networks and the movements among habitats can be critical for the life history of many fish species, and understanding of the patterns of movement is central to managing populations, communities, and the landscapes they use. We combined passive integrated transponder tagging over 4 years and strontium isotopes in otoliths to demonstrate that 25% of the mountain whitefish (Prosopium williamsoni) sampled moved between the Methow and Columbia rivers, Washington, USA. Seasonal migrations downstream from the Methow River to the Columbia River to overwinter occurred in autumn and upstream movements in the spring. We observed migration was common during the first year of life, with migrants being larger than nonmigrants. However, growth between migrants and nonmigrants was similar. Water temperature was positively related to the proportion of migrants and negatively related to the timing of migration, but neither was related to discharge. The broad spatio-temporal movements we observed suggest mountain whitefish, and likely other nonanadromous fish, require distant habitats and also suggests that management and conservation strategies to keep connectivity of large river networks are imperative.
Acidobacteria from oligotrophic soil from the Cerrado can grow in a wide range of carbon source concentrations
Authors: de Castro Virgilio Hipólito Lemos , Schroeder Luis Felipe , Quirino Betania Ferraz , Kruger Ricardo Henrique , Barreto Cristine Chaves
Published: October 2013

Soils from the Brazilian Cerrado are nutrient-poor, acidic, and aluminum-rich. A previous study revealed that members of the phylum Acidobacteria were predominant in these oligotrophic soils. Five acidobacteria from Cerrado soil were isolated on VL-55 medium containing 0.05% of xylan as carbon source. All isolates belong to the Acidobacteria subdivision 1, and their 16S rRNA showed similarities of 94.2%–96% with Acidobacterium capsulatum or 98.6% with Edaphobacter aggregans. All isolates were able to sustain growth in a wide range of carbon source concentrations. Growth occurred in all concentrations of arabinose, dextrose, and xylose; only one isolate did not grow on fructose. Isolates grew poorly on N-acetyl-d-glucosamine at all concentrations tested. In general, increasing concentrations of these monosaccharides did not inhibit growth rates. Isolates exhibited growth on solid medium containing xylan, carboxymethyl cellulose, and colloidal chitin; however, growth was observed on solid medium that did not contain these polysaccharides. These isolates may be able to use the solidifying agents tested (gellan gum or agar) as carbon source. This interpretation is supported by the absence of growth in liquid media containing chitin or carboxymethyl cellulose at 0.05% as sole carbon source, whereas growth in the same conditions using xylan was confirmed.
Pseudo-random bit generator based on lag time series
Authors: García-Martínez M. , Campos-Cantón E.
Published: October 2013

In this paper, we present a pseudo-random bit generator (PRBG) based on two lag time series of the logistic map using positive and negative values in the bifurcation parameter. In order to hidden the map used to build the pseudo-random series we have used a delay in the generation of time series. These new series when they are mapped xn against xn+1 present a cloud of points unrelated to the logistic map. Finally, the pseudo-random sequences have been tested with the suite of NIST giving satisfactory results for use in stream ciphers.
AN EXTRACTION AND EXPANSION APPROACH FOR GRAPH COLORING
Authors: WU QINGHUA , HAO JIN-KAO
Published: October 2013

This paper presents an extraction and expansion approach for the graph coloring problem. The extraction phase transforms a large graph into a sequence of progressively smaller graphs by removing large independent sets from the graph. The expansion phase starts by generating an approximate coloring for the smallest graph in the sequence. Then it expands the smallest graph by progressively adding back the extracted independent sets and determine a coloring for each intermediate graph. To color each graph, a simple perturbation based tabu search algorithm is used. The proposed approach is evaluated on the DIMACS challenge benchmarks showing competitive results in comparison with the state-of-the-art methods.
LHCf DETECTOR PERFORMANCE DURING THE 2009–2010 LHC RUN
Authors:   (The LHCf Collaboration), ADRIANI O. , BONECHI L. , BONGI M. , CASTELLINI G. , D'ALESSANDRO R. , HAGUENAUER M. , ISO T. , ITOW Y. , KASAHARA K. , KAWADE K. , MASUDA K. , MENJO H. , MITSUKA G. , MURAKI Y. , NODA K. , PAPINI P. , PERROT A.-L. , RICCIARINI S. , SAKO T. , SHIMIZU Y. , SUZUKI T. , TAMURA T. , TORII S. , TRICOMI A. , TURNER W. C.
Published: October 2013

Large Hadron Collider forward (LHCf) has successfully completed the operation during the LHC 2009–2010 period and the detectors were removed in July 2010. The event trigger, data analysis and background have been intensively studied in order to derive inclusive single photon and π0 spectra. In this paper, the details of these intensive studies are described.
NONCOMMUTATIVE GAUGE THEORIES: MODEL FOR HODGE THEORY
Authors: UPADHYAY SUDHAKER , MANDAL BHABANI PRASAD
Published: October 2013

The nilpotent Becchi–Rouet–Stora–Tyutin (BRST), anti-BRST, dual-BRST and anti-dual-BRST symmetry transformations are constructed in the context of noncommutative (NC) 1-form as well as 2-form gauge theories. The corresponding Noether's charges for these symmetries on the Moyal plane are shown to satisfy the same algebra, as by the de Rham cohomological operators of differential geometry. The Hodge decomposition theorem on compact manifold is also studied. We show that noncommutative gauge theories are field theoretic models for Hodge theory.
FIELD REDEFINITION AND RENORMALIZABILITY IN SCALAR FIELD THEORIES
Authors: MOHAMMEDI N.
Published: October 2013

We have addressed the issue of field redefinition in connection with renormalizability. Our study is restricted to theories of interacting scalar fields. We have, in particular, shown that if a theory is renormalizable in the usual power-counting sense then it remains renormalizable in the same sense after a change of variables. This is due to the use of the powerful method of the background field expansion. In the case of a single complex scalar field, it turns out that the determination of the counterterms is much simpler when polar coordinates are used. We illustrate this by carrying out a one-loop calculation in the latter case.
POLYNOMIAL SOLUTIONS OF HEUN EQUATION DESCRIBING FERMIONS IN GRAPHENE
Authors: DARIESCU MARINA-AURA , DARIESCU CIPRIAN
Published: October 2013

The wavefunctions describing the massless fermions evolving in a static magnetic field orthogonal to a radially planar electric field are obtained, as solutions to Dirac equation. In the case of the magnetic field alone, the corresponding HeunB confluent functions turn into the usual Hermite polynomials and the energy spectrum has the familiar form which has been reported for graphene samples. Within a more involved analysis with both electric and magnetic orthogonal static fields, we compute the conserved current density component and the quantized off-diagonal conductivity.
QUANTUM DYNAMICS WITH AN ENSEMBLE OF HAMILTONIANS
Authors: RAHMANI ARMIN
Published: October 2013

We review recent progress in the nonequilibrium dynamics of thermally isolated many-body quantum systems, evolving with an ensemble of Hamiltonians as opposed to deterministic evolution with a single time-dependent Hamiltonian. Such questions arise in (i) quantum dynamics of disordered systems, where different realizations of disorder give rise to an ensemble of real-time quantum evolutions, (ii) quantum evolution with noisy Hamiltonians (temporal disorder), which leads to stochastic Schrödinger equations, and, (iii) in the broader context of quantum optimal control, where one needs to analyze an ensemble of permissible protocols in order to find one that optimizes a given figure of merit. The theme of ensemble quantum evolution appears in several emerging new directions in noneqilibrium quantum dynamics of thermally isolated many-body systems, which include many-body localization, noise-driven systems, and shortcuts to adiabaticity.
ENHANCING THE ACCURACY OF LICENSE PLATE RECOGNITION SYSTEMS WITH THE ANGLE RECOVERY METHOD
Authors: TARNG WERNHUAR , LI CHIEN-LUNG
Published: October 2013

The motor vehicle is an important way of transportation for modern people, and its license plate is just like our identification cards which can be used for effective management of motor vehicles. Hence, the development of a recognition system for license plates can reduce the workload of managing motor vehicles. A license plate recognition system based on computer vision often causes recognition errors due to the plate's angle problem and thus needs to be assisted by manual recognition. In this study, a recovery method for license plate images with large angles is proposed based on perspective projection to increase the recognition accuracy. The experimental results show that applying the angle recovery method to a license plate recognition system can reduce its errors, especially for license plate images with large angles. For the case of small angles, a recognition rate of 89% can be achieved by the angle recovery method, slightly higher than that of the plane rotation method (86%). For the case of a wide range of different angles, the average recognition rate achieved by the angle recovery method is 87.5%, much higher than that of the plane rotation method (57.5%). Thus, the angle recovery method is effective for enhancing the accuracy of license plate recognition systems.
ENGINEERING INNOVATION-RELATED KNOWLEDGE: HOW A CORE ONTOLOGY MAKES INNOVATIONS RETRIEVABLE FOR INNOVATION SEEKERS
Authors: LIPPMANN TORBEN
Published: October 2013

The motivation of this paper is to name the central lines of development in the research field of innovation-related knowledge engineering. This helps to define the starting point for an urgently required interdisciplinary academic discussion about the design of a core ontology for innovations. A review about the currently known ontologies for innovation emphasizes the need for engineering a core ontology for innovations based on a valid consensual understanding of the term innovation. In a universally applicable conception, innovation is characterized as a (re-) combination of purposes and means. A transmission of this conceptualization is presented, visualized and its usage shown through the ontology InnOnto. The paper concludes with implications for future research tasks in the field of innovation-related knowledge engineering.
Annihilation and coalescence on binary trees
Authors: Benjamini Itai , Lima Yuri
Published: October 2013

An infection spreads in a binary tree [Formula: see text] of height n as follows: initially, each leaf is either infected by one of k states or it is not infected at all. The infection state of each leaf is independently distributed according to a probability vector p = (p1, …, pk+1). The remaining nodes become infected or not via annihilation and coalescence: nodes whose two children have the same state (infected or not) are infected (or not) by this state; nodes whose two children have different states are not infected; nodes such that only one of the children is infected are infected by this state. In this paper we characterize, for every p, the limiting distribution at the root node of [Formula: see text] as n goes to infinity.

We also consider a variant of the model when k = 2 and a mutation can happen, with a fixed probability q, at each infection step. We characterize, in terms of p and q, the limiting distribution at the root node of [Formula: see text] as n goes to infinity.

The distribution at the root node is driven by a dynamical system, and the proofs rely on the analysis of this dynamics.
MULTIOBJECTIVE DECISION SUPPORT FOR THE KWANZA RIVER MANAGEMENT
Authors: MARIE KIOMBO J. , CANO JAVIER , RÍOS INSUA DAVID , ARROYO ÓSCAR
Published: October 2013

Water management has become a challenging problem worldwide, especially in developing countries, due to several reasons including the growing scarcity of natural water resources; a demographic explosion in many urban settlements, followed by a rapid urbanization and industrialization of neighboring areas; and the inherent increase in the demand of energy and natural fresh water for human consumption and agricultural developments. The Kwanza river, the longest and most plentiful in Angola, is a paradigmatic case, as it is one of the main sources of wealth in that country. Many people base, direct or indirectly, their living on its water, and many economical activities, including energy production, depend also on its stream. We provide a model for the multiobjective multipurpose management of the Kwanza river. The problem is complicated by the need to take into account uncertainty in various involved processes, to plan over a long period of time, and the presence of several conflicting objectives. We describe also a decision support system implementing our model.
MULTI-STAGE TECHNIQUE 'PAKS' FOR MULTIPLE CRITERIA DECISION AIDING
Authors: PETROVSKY ALEXEY B. , ROYZENSON GREGORY V.
Published: October 2013

This paper describes a new multi-stage technique PAKS (the abbreviation of Russian words: Consequent Aggregation of Classified Situations) for sorting multi-attribute objects by a group. Based on decision maker preferences, this technique provides a hierarchical aggregation of a large number of initial attributes into a smaller number of criteria, thus reducing the dimension of the attribute space progressively, using various tools of verbal decision analysis. The consequent aggregation of attributes allows generating manifold lists of composite criteria with numerical and/or verbal scales, finding and analyzing the most preferable solution of a decision problem. The technique was applied to evaluate efficiency of R&D projects, which were assessed by several experts on many qualitative criteria and subsidized by the Russian Foundation for Basic Research.
ENHANCEMENT OF COGNITIVE CREATIVITY BY DIVERSITY CLUSTERING
Authors: PETRY FREDERICK E. , YAGER RONALD R.
Published: October 2013

In this paper, formation of diverse groups of individuals based on attributes and two diversity measures are discussed. The formation of clusters in a diversity space is described. An algorithm is given for diverse clustering based on separation in the space and not the nearness using application based diversity thresholds and number of clusters.
STATUS OF SEISMIC ANALYSIS METHODS FOR TRAFFIC TUNNEL AND THEIR APPLICABILITY SUGGESTIONS IN CHINA
Authors: HE CHUAN , GENG PING , YAN QIXIANG , FENG KUN
Published: October 2013

Located between the Eurasia seismic zone and the circum-Pacific seismic belt, China is the largest continent shallow earthquake area around the world by the frequent earthquake activities. And great quantities of tunnels are located in high earthquake intensity area of China. As one of the main structure of the national lifeline, the seismic analysis methods of tunnel must be paid high attention. Based on seismic response characteristics of the traffic tunnel structure, this paper provides a synthesis of the current state of knowledge in the area of seismic analysis for tunnel, including the seismic design criteria, earthquake effects, tunnel seismic behaviors, and the seismic analysis procedure of tunnel. It focuses on analysis methods of tunnel subjected to seismic motion. There are three major seismic analysis methods normally used in tunnel structures; they are seismic coefficient method, seismic deformation method and dynamic response method. The basic principles of the three methods are described in this paper. Based on the different mechanical characteristics between cross-section and axial direction, the proper seismic analysis methods in the two directions are put forward according to the different construction method of tunnel. The research results will provide reference for seismic analysis of traffic tunnel.