bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental Identification of Dynamic Force Coefficients for a 110 mm Compliantly Damped Hybrid Gas Bearing
Authors: Delgado Adolfo
Published: September 2014

Compliant hybrid gas bearings combine key enabling features from both fixed geometry externally pressurized gas bearings and compliant foil bearings. The compliant hybrid bearing relies on both hydrostatic and hydrodynamic film pressures to generate load capacity and stiffness to the rotor system, while providing damping through integrally mounted metal mesh bearing support dampers. This paper presents experimentally identified force coefficients for a 110 mm compliantly damped gas bearing using a controlled-motion test rig. Test parameters include hydrostatic inlet pressure, excitation frequency, and rotor speed. The experiments were structured to evaluate the feasibility of implementing these bearings in large size turbomachinery. Dynamic test results indicate weak dependency of equivalent direct stiffness coefficients to most test parameters except for frequency and speed, where higher speeds and excitation frequency decreased equivalent bearing stiffness values. The bearing system equivalent direct damping was negatively impacted by increased inlet pressure and excitation frequency, while the cross-coupled force coefficients showed values an order of magnitude lower than the direct coefficients. The experiments also include orbital excitations to simulate unbalance response representative of a target machine while synchronously traversing a critical speed. The results indicate that the gas bearing can accommodate vibration levels larger than the set bore clearance while maintaining satisfactory damping levels.
Gas Turbine Fault Classification Using Probability Density Estimation
Authors: Loboda Igor
Published: September 2014

Diagnostics is an important aspect of a condition based maintenance program. To develop an effective gas turbine monitoring system in short time, the recommendations on how to optimally design every system algorithm are required. This paper deals with choosing a proper fault classification technique for gas turbine monitoring systems.

To classify gas path faults, different artificial neural networks are typically employed. Among them the Multilayer Perceptron (MLP) is the mostly used. Some comparative studies referred to in the introduction show that the MLP and some other techniques yield practically the same classification accuracy on average for all faults. That is why in addition to the average accuracy, more criteria to choose the best technique are required. Since techniques like Probabilistic Neural Network (PNN), Parzen Window (PW) and k-Nearest Neighbor (K-NN) provide a confidence probability for every diagnostic decision, the presence of this important property can be such a criterion. The confidence probability in these techniques is computed through estimating a probability density for patterns of each concerned fault class.

The present study compares all mentioned techniques and their variations using as criteria both the average accuracy and availability of the confidence probability. To compute them for each technique, a special testing procedure simulates numerous diagnosis cycles corresponding to different fault classes and fault severities. In addition to the criteria themselves, criteria imprecision due to a finite number of the diagnosis cycles is computed and involved into selecting the best technique.
Numerical Study on Tip Leakage Flow Structure of an Axial Flow Compressor Rotor
Authors: Zhang Chenkai , Hu Jun , Wang Zhiqiang , Yan Wei , Yin Chao , Gao Xiang
Published: September 2014

To deepen the knowledge of tip leakage flow/vortex flow structure in the tip clearance of axial compressor rotors, this paper presents steady numerical studies on a subsonic rotor. The rotor and its related low-speed large-scale repeating-stage axial compressor are used for low-speed model testing of a modern high-pressure compressor. Results were first compared with available experimental data to validate adopted numerical method. Then complex endwall flow structure and flow loss mechanism at design operating point were studied. At last, comparisons were made for tip leakage vortex structure, interface of the leakage flow/main flow, endwall blockage and loss between design and near-stall operating points. Results show that only the spilled flows below 62.5% clearance height at the leading edge will roll into tip leakage vortex for this rotor. In addition, tip leakage vortex plays a secondary important role for higher positions, where secondary leakage flow occurs and occupies broader chordwise range. Although tip leakage vortex would expand and strongly mix with the mainflow when it propagates downstream, which leads to a rapid reduction of the normalized streamwise vorticity, the value of the normalized helicity shows that concentrated vortex feature is still maintained.
Modelling the Formation of Oxides of Nitrogen in Premix Combustion by Extending Tabulated Chemistry With Algebraic Relations
Authors: Collonval Frederic B. A. , Polifke Wolfgang
Published: September 2014

Models of finite rate combustion chemistry based on tabulation have been found to be efficient and accurate for a broad range of fuel and flame configurations. However, the modelling of formation of oxides of nitrogen remains a challenging issue. Even recent developments that take into account heat losses do not provide accurate prediction of NOx species despite a very good match for major species and temperature. The present paper introduces a model based on a chemical lookup-table for the NO formation rate in the preheat, initiation and fuel consumption region of a premix flame combined with algebraic relations in the post-flame area, thus reducing advantageously the tabulated information. This model is applied to a premixed laminar burner and compared to previous models based on tabulated chemistry.
Effect of residual stress on replication fidelity with nanoimprint
Authors: Papenheim Marc , Dhima Khalid , Wang Si , Steinberg Christian , Scheer Hella-Christin , Saupe Jens , Schönfeld Maik , Grimm Jürgen
Published: September 2014

Relief of residual stress in an imprinted polymer may affect the replication fidelity by leading to recovery. The level of stress induced in the polymer depends on the method of imprint. For example, a “soft” imprint with an elastomeric stamp uses capillary forces to fill the cavities whereas a “hard” imprint with a rigid stamp relies on external pressure. To study the effect of residual stress after imprint, both methods are applied with different imprint times to vary the level of residual stress, as the stress remaining relaxes with imprint time. To visualize the residual stress a temperature treatment is performed after imprint. This temperature treatment allows recovery within a convenient experimental time. A comparison of the shape of the imprinted structures before and after temperature treatment clearly shows that with a hard imprint at short imprint times a considerable amount of stress remains in the polymer, in particular when the residual layer is thin and the imprinted stamp structures are wide. With a soft imprint residual stress is not evident. Similar results are obtained with a thermoplastic material and a crosslinking material (SU-8); however, with the latter recovery remains limited due to a decrease of mobility during crosslinking. Residual stress is of major importance for the replication fidelity with short imprint processes.
Improving x‐ray fluorescence signal for benchtop polychromatic cone‐beam x‐ray fluorescence computed tomography by incident x‐ray spectrum optimization: A Monte Carlo study
Authors: Manohar Nivedh , Jones Bernard L. , Cho Sang Hyun
Published: September 2014

Purpose:

To develop an accurate and comprehensive Monte Carlo (MC) model of an experimental benchtop polychromatic cone‐beam x‐ray fluorescence computed tomography (XFCT) setup and apply this MC model to optimize incident x‐ray spectrum for improving production/detection of x‐ray fluorescence photons from gold nanoparticles (GNPs).

Methods:

A detailed MC model, based on an experimental XFCT system, was created using the Monte Carlo N‐Particle (MCNP) transport code. The model was validated by comparing MC results including x‐ray fluorescence (XRF) and scatter photon spectra with measured data obtained under identical conditions using 105 kVp cone‐beam x‐rays filtered by either 1 mm of lead (Pb) or 0.9 mm of tin (Sn). After validation, the model was used to investigate the effects of additional filtration of the incident beam with Pb and Sn. Supplementary incident x‐ray spectra, representing heavier filtration (Pb: 2 and 3 mm; Sn: 1, 2, and 3 mm) were computationally generated and used with the model to obtain XRF/scatter spectra. Quasimonochromatic incident x‐ray spectra (81, 85, 90, 95, and 100 keV with 10 keV full width at half maximum) were also investigated to determine the ideal energy for distinguishing gold XRF signal from the scatter background. Fluorescence signal‐to‐dose ratio (FSDR) and fluorescence‐normalized scan time (FNST) were used as metrics to assess results.

Results:

Calculated XRF/scatter spectra for 1‐mm Pb and 0.9‐mm Sn filters matched (r ≥ 0.996) experimental measurements. Calculated spectra representing additional filtration for both filter materials showed that the spectral hardening improved the FSDR at the expense of requiring a much longer FNST. In general, using Sn instead of Pb, at a given filter thickness, allowed an increase of up to 20% in FSDR, more prominent gold XRF peaks, and up to an order of magnitude decrease in FNST. Simulations using quasimonochromatic spectra suggested that increasing source x‐ray energy, in the investigated range of 81–100 keV, increased the FSDR up to a factor of 20, compared to 1 mm Pb, and further facilitated separation of gold XRF peaks from the scatter background.

Conclusions:

A detailed MC model of an experimental benchtop XFCT system has been developed and validated. In exemplary calculations to illustrate the usefulness of this model, it was shown that potential use of quasimonochromatic spectra or judicious choice of filter material/thickness to tailor the spectrum of a polychromatic x‐ray source can significantly improve the performance of benchtop XFCT, while considering trade‐offs between FSDR and FNST. As demonstrated, the current MC model is a reliable and powerful computational tool that can greatly expedite the further development of a benchtop XFCT system for routine preclinical molecular imaging with GNPs and other metal probes.
GABA/glutamate co-release controls habenula output and is modified by antidepressant treatment
Authors: Shabel Steven J. , Proulx Christophe D. , Piriz Joaquin , Malinow Roberto
Published: September 2014

A pathway that controls our mood

A brain area called the lateral habenula is involved in negative motivation and may thus play a role in depression. Shabel
et al.
investigated synaptic transmission in a brain pathway to the lateral habenula that transmits disappointment signals. Surprisingly, they found the simultaneous release of two antagonistic substances, glutamate and GABA, from individual nerve cells. In an animal model of depression, GABA release was reduced in this pathway. A widely used antidepressant drug, however, increased GABA co-release. These results reveal an unusual synaptic mechanism that affects lateral habenula activity. This mechanism may be instrumental for regulating the emotional impact of disappointment.

Science
, this issue p.
1494
IRBIT is a novel regulator of ribonucleotide reductase in higher eukaryotes
Authors: Arnaoutov Alexei , Dasso Mary
Published: September 2014

Regulating DNA building blocks

The bulding blocks of DNA, deoxynucleotide triphosphates, are synthesized by the enzyme ribonucleotide reductase (RNR). Its central role in DNA synthesis and its aberrant expression in tumors have made it an important anticancer target, but nucleoside analog inhibitors of RNR can have adverse side effects. Arnaoutov and Dasso identify IRBIT (IP
3
-receptor-binding protein released with inositol 1,4,5-trisphosphate) as an RNR-binding protein. IRBIT regulates the activity of RNR by stabilizing the inactive form bound to deoxyadenosine triphosphate in the low-affinity A site. In turn, phosophorylation of IRBIT regulates its RNR-binding activity. IRBIT provides a new target for RNR inhibition that might avoid some of the side effects of current drugs.

Science
, this issue p.
1512
Be one of the first
Authors: McNutt Marcia
Published: September 2014

On 3 July 1880, “a weekly journal of scientific progress” published its first research articles under the banner
Science
. From that original print medium, the inaugural set of papers has been reprinted, photocopied, posted online, converted to PDF, and even etched in glass blocks to serve as special gifts. Being part of the vanguard is indeed a privilege, and opportunities to be one of the first are rare. For that reason, I proudly announce that
Science Advances
, a new open-access journal for all of the sciences, officially joins the
Science
family of journals (
Science, Science Translational Medicine
, and
Science Signaling
) and is now accepting submissions (go to
www.scienceadvances.org
). In February 2015, the inaugural papers will be released, heralding the start of something big in scope, reach, and influence.
All eyes on shooting stars
Authors: Hand Eric
Published: September 2014

By tracking meteorite falls, camera and radar networks help searchers find precious fragments.
Who are the science stars of Twitter?
Authors: You Jia
Published: September 2014

Science communicators and some highly cited researchers, but few women, make top 50 most followed list.
Association between Serotype-Specific Antibody Response and Serotype Characteristics in Patients with Pneumococcal Pneumonia, with Special Reference to Degree of Encapsulation and Invasive Potential
Authors: Athlin Simon , Kaltoft Margit , Slotved Hans-Christian , Herrmann Björn , Holmberg Hans , Konradsen Helle Bossen , Strålin Kristoffer
Published: September 2014

We studied the immunoglobulin (Ig) response to causative serotype-specific capsular polysaccharides in adult pneumococcal pneumonia patients. The serotypes were grouped according to their degree of encapsulation and invasive potential. Seventy patients with pneumococcal pneumonia, 20 of whom were bacteremic, were prospectively studied. All pneumococcal isolates from the patients were serotyped, and the Ig titers to the homologous serotype were determined in acute- and convalescent-phase sera using a serotype-specific enzyme-linked immunosorbent assay. The Ig titers were lower in bacteremic cases than in nonbacteremic cases (P< 0.042). The Ig titer ratio (convalescent/acute titer) was ≥2 in 33 patients, 1 to 1.99 in 20 patients, and <1 in 17 patients. Patients ≥65 years old had a lower median Ig titer ratio than did younger patients (P< 0.031). The patients with serotypes with a thin capsule (1, 4, 7F, 9N, 9V, and 14) and medium/high invasive potential (1, 4, 7F, 9N, 9V, 14, and 18C) had higher Ig titer ratios than did patients with serotypes with a thick capsule (3, 6B, 11A, 18C, 19A, 19F, and 23F) and low invasive potential (3, 6B, 19A, 19F, and 23F) (P< 0.05 for both comparisons after adjustment for age). Ig titer ratios of <1 were predominantly noted in patients with serotypes with a thick capsule. In 8 patients with pneumococcal DNA detected in plasma, the three patients with the highest DNA load had the lowest Ig titer ratios. In conclusion, a high antibody response was associated with serotypes with a thin capsule and medium/high invasive potential, although a low antibody response was associated with serotypes with a thick capsule and a high pneumococcal plasma load.
Determination of Specific Antibody Responses to the Six Species of Ebola and Marburg Viruses by Multiplexed Protein Microarrays
Authors: Kamata Teddy , Natesan Mohan , Warfield Kelly , Aman M. Javad , Ulrich Robert G.
Published: September 2014

Infectious hemorrhagic fevers caused by the Marburg and Ebola filoviruses result in human mortality rates of up to 90%, and there are no effective vaccines or therapeutics available for clinical use. The highly infectious and lethal nature of these viruses highlights the need for reliable and sensitive diagnostic methods. We assembled a protein microarray displaying nucleoprotein (NP), virion protein 40 (VP40), and glycoprotein (GP) antigens from isolates representing the six species of filoviruses for use as a surveillance and diagnostic platform. Using the microarrays, we examined serum antibody responses of rhesus macaques vaccinated with trivalent (GP, NP, and VP40) virus-like particles (VLP) prior to infection with the Marburg virus (MARV) (i.e.,Marburg marburgvirus) or the Zaire virus (ZEBOV) (i.e.,Zaire ebolavirus). The microarray-based assay detected a significant increase in antigen-specific IgG resulting from immunization, while a greater level of antibody responses resulted from challenge of the vaccinated animals with ZEBOV or MARV. Further, while antibody cross-reactivities were observed among NPs and VP40s of Ebola viruses, antibody recognition of GPs was very specific. The performance of mucin-like domain fragments of GP (GP mucin) expressed inEscherichia coliwas compared to that of GP ectodomains produced in eukaryotic cells. Based on results with ZEBOV and MARV proteins, antibody recognition of GP mucins that were deficient in posttranslational modifications was comparable to that of the eukaryotic cell-expressed GP ectodomains in assay performance. We conclude that the described protein microarray may translate into a sensitive assay for diagnosis and serological surveillance of infections caused by multiple species of filoviruses.
Characterization of T-Cell Responses to Conserved Regions of the HIV-1 Proteome in BALB/c Mice
Authors: Ondondo Beatrice , Abdul-Jawad Sultan , Bridgeman Anne , Hanke Tomáš
Published: September 2014

A likely requirement for a protective vaccine against human immunodeficiency virus type 1 (HIV-1)/AIDS is, in addition to eliciting antibody responses, induction of effective T cells. To tackle HIV-1 diversity by T-cell vaccines, we designed an immunogen, HIVconsv, derived from the most functionally conserved regions of the HIV-1 proteome and demonstrated its high immunogenicity in humans and rhesus macaques when delivered by regimens combining plasmid DNA, nonreplicating simian (chimpanzee) adenovirus ChAdV-63, and nonreplicating modified vaccinia virus Ankara (MVA) as vectors. Here, we aimed to increase the decision power for iterative improvements of this vaccine strategy in the BALB/c mouse model. First, we found that prolonging the period after the ChAdV63.HIVconsv prime up to 6 weeks increased the frequencies of HIV-1-specific, gamma interferon (IFN-γ)-producing T cells induced by the MVA.HIVconsv boost. Induction of strong responses allowed us to map comprehensively the H-2d-restricted T-cell responses to these regions and identified 8 HIVconsv peptides, of which three did not contain a previously described epitope and were therefore considered novel. Induced effector T cells were oligofunctional and lysed sensitized targetsin vitro. Our study therefore provides additional tools for studying and optimizing vaccine regimens in this commonly used small animal model, which will in turn guide vaccine improvements in more expensive nonhuman primate and human clinical trials.
Identification of a Novel RNA Virus Lethal to Tilapia
Authors: Eyngor Marina , Zamostiano Rachel , Kembou Tsofack Japhette Esther , Berkowitz Asaf , Bercovier Hillel , Tinman Simon , Lev Menachem , Hurvitz Avshalom , Galeotti Marco , Bacharach Eran , Eldar Avi
Published: September 2014

Tilapines are important for the sustainability of ecological systems and serve as the second most important group of farmed fish worldwide. Significant mortality of wild and cultured tilapia has been observed recently in Israel. The etiological agent of this disease, a novel RNA virus, is described here, and procedures allowing its isolation and detection are revealed. The virus, denominated tilapia lake virus (TiLV), was propagated in primary tilapia brain cells or in an E-11 cell line, and it induced a cytopathic effect at 5 to 10 days postinfection. Electron microscopy revealed enveloped icosahedral particles of 55 to 75 nm. Low-passage TiLV, injected intraperitoneally in tilapia, induced a disease resembling the natural disease, which typically presents with lethargy, ocular alterations, and skin erosions, with >80% mortality. Histological changes included congestion of the internal organs (kidneys and brain) with foci of gliosis and perivascular cuffing of lymphocytes in the brain cortex; ocular inflammation included endophthalmitis and cataractous changes of the lens. The cohabitation of healthy and diseased fish demonstrated that the disease is contagious and that mortalities (80 to 100%) occur within a few days. Fish surviving the initial mortality were immune to further TiLV infections, suggesting the mounting of a protective immune response. Screening cDNA libraries identified a TiLV-specific sequence, allowing the design of a PCR-based diagnostic test. This test enables the specific identification of TiLV in tilapines and should help control the spread of this virus worldwide.
Characteristics of Patients Recently Infected with HIV-1 Non-B Subtypes in France: a Nested Study within the Mandatory Notification System for New HIV Diagnoses
Authors: Brand Denys , Moreau Alain , Cazein Françoise , Lot Florence , Pillonel Josiane , Brunet Sylvie , Thierry Damien , Le Vu Stéphane , Plantier Jean-Christophe , Semaille Caroline , Barin Francis
Published: September 2014

The presence of HIV-1 non-B subtypes in Western Europe is commonly attributed to migration of individuals from non-European countries, but the possible role of domestic infections with non-B subtypes is not well investigated. The French mandatory anonymous reporting system for HIV is linked to a virological surveillance using assays for recent infection (<6 months) and serotyping. During the first semester of years 2007 to 2010, any sample corresponding to a non-B recent infection was analyzed by sequencing a 415-bp
env
region, followed by phylogenetic analysis and search for transmission clusters. Two hundred thirty-three recent HIV-1 infections with non-B variants were identified. They involved 5 subtypes and 7 circulating recombinant forms (CRFs). Ninety-two cases (39.5%) were due to heterosexual transmissions, of which 39 occurred in patients born in France. Eighty-five cases (36.5%) were identified in men having sex with men (MSM). Forty-three recent non-B infections (18.5%) segregated into 14 clusters, MSM being involved in 11 of them. Clustered transmission events included 2 to 7 cases per cluster. The largest cluster involved MSM infected by a CRF02_AG variant. In conclusion, we found that the spread of non-B subtypes in France occurs in individuals of French origin and that MSM are particularly involved in this dynamic.
Rapid Diagnosis of Cryptococcal Meningitis by Use of Lateral Flow Assay on Cerebrospinal Fluid Samples: Influence of the High-Dose “Hook” Effect
Authors: Lourens Adré , Jarvis Joseph N. , Meintjes Graeme , Samuel Catherine M.
Published: September 2014

Cryptococcal meningitis is the most frequent cause of meningitis and a major cause of mortality in HIV-infected adults in Africa. This study evaluated the performance of the lateral flow assay (LFA) on cerebrospinal fluid (CSF) samples for the diagnosis of cryptococcal meningitis against that of existing diagnostic tests. LFA performed on 465 undiluted CSF samples had a sensitivity of 91%. When the LFA was paired with Gram staining, a sensitivity of 100% was achieved after implementation of a dilution step for samples with negative LFA results and the presence of yeasts on microscopy. Microscopy is essential for preventing the reporting of false-negative results due to the high-dose “hook” effect.
Inconsistency of Phenotypic and Genomic Characteristics of Campylobacter fetus Subspecies Requires Reevaluation of Current Diagnostics
Authors: van der Graaf-van Bloois Linda , Miller William G. , Yee Emma , Rijnsburger Martine , Wagenaar Jaap A. , Duim Birgitta
Published: September 2014

Classifications of the
Campylobacter fetus
subspecies
fetus
and
venerealis
were first described in 1959 and were based on the source of isolation (intestinal versus genital) and the ability of the strains to proliferate in the genital tract of cows. Two phenotypic assays (1% glycine tolerance and H
2
S production) were described to differentiate the subspecies. Multiple molecular assays have been applied to differentiate the
C. fetus
subspecies, but none of these tests is consistent with the phenotypic identification methods. In this study, we defined the core genome and accessory genes of
C. fetus
, which are based on the closed genomes of five
C. fetus
strains. Phylogenetic analysis of the core genomes of 23
C. fetus
strains of the two subspecies showed a division into two clusters. The phylogenetic core genome clusters were not consistent with the phenotypic classifications of the
C. fetus
subspecies. However, they were consistent with the molecular characteristics of the strains, which were determined by multilocus sequence typing,
sap
typing, and the presence/absence of insertion sequences and a type I restriction modification system. The similarity of the genome characteristics of three of the phenotypically defined
C. fetus
subsp.
fetus
strains to
C. fetus
subsp.
venerealis
strains, when considering the core genome and accessory genes, requires a critical evaluation of the clinical relevance of
C. fetus
subspecies identification by phenotypic assays.
Improved Diagnosis of Infection Associated with Osteosynthesis by Use of Sonication of Fracture Fixation Implants
Authors: Yano Maysa Harumi , Klautau Giselle Burlamaqui , da Silva Cely Barreto , Nigro Stanley , Avanzi Osmar , Mercadante Marcelo Tomanink , Salles Mauro Jose Costa
Published: September 2014

Previous studies have shown that sonication fluid cultures from removed orthopedic devices improved the microbiological diagnosis of orthopedic implant-associated infections; however, few of these investigations have applied sonication to the removed fracture fixation devices to evaluate its utility for the diagnosis of osteosynthesis-associated infection (OAI). We compared sonication fluid to conventional tissue cultures from 180 subjects with different sizes of plates and screws (
n
= 156), spinal implants (
n
= 26), and intramedullary nails (
n
= 3), of whom 125 and 55 subjects had OAI and noninfected osteosynthesis (NIO), respectively. The sensitivity for detecting OAI was 90.4% for sonication fluid culture and 56.8% for periprosthetic tissue cultures (
P
< 0.05), and the specificities were 90.9% and 96.4%, respectively. Sonication fluid culture detected more pathogens than peri-implant tissue culture (113 versus 71;
P
< 0.001), while polymicrobial infections were diagnosed by sonication fluid cultures and tissue cultures in 20.8% and 8% (
P
< 0.001), respectively. Microbiological diagnosis was achieved exclusively by sonication fluid cultures for 47 (90.4%) subjects, and among them, 18 (38.3%) had previously received antibiotics, whereas in five (9.6%) infected subjects, tissue culture was positive and the sonication fluid culture was negative. Among 39 (31.2%) OAI cases receiving antibiotics, the identification of the organisms occurred in 38.5% and 82.1% of the tissue and sonication fluid cultures, respectively (
P
< 0.049). We demonstrated that sonication fluid culture from removed osteosyntheses has the potential for improving the microbiological diagnosis of OAI.
Epididymitis Caused by Coxsackievirus A6 in Association with Hand, Foot, and Mouth Disease
Authors: Vuorinen Tytti , Österback Riikka , Kuisma Jani , Ylipalosaari Pekka
Published: September 2014

Coxsackievirus A6 (CV-A6) caused hand, foot, and mouth disease (HFMD) with a unique manifestation of epididymitis. The patient underwent operation due to suspicion of testicular torsion. Epididymitis was diagnosed by ultrasound examination. Enterovirus was detected from epididymal fluid by PCR and typed by partial sequencing of viral protein 1 as CV-A6.
Amino Acid Changes in the Influenza A Virus PA Protein That Attenuate Avian H5N1 Viruses in Mammals
Authors: Fan Shufang , Hatta Masato , Kim Jin Hyun , Le Mai Quynh , Neumann Gabriele , Kawaoka Yoshihiro
Published: September 2014

The influenza viral polymerase complex affects host tropism and pathogenicity. In particular, several amino acids in the PB2 polymerase subunit are essential for the efficient replication of avian influenza viruses in mammals. The PA polymerase subunit also contributes to host range and pathogenicity. Here, we report that the PA proteins of several highly pathogenic avian H5N1 viruses have attenuating properties in mammalian cells and that the attenuating phenotype is conferred by strain-specific amino acid changes. Specifically, lysine at position 185 of A/duck/Vietnam/TY165/2010 (TY165; H5N1) PA induced strongly attenuating effects
in vitro
and
in vivo
. More importantly, the introduction of the arginine residue commonly found at this position in PA significantly increased the viral polymerase activity of TY165 in mammalian cells and its virulence and pathogenicity in mice. These findings demonstrate that the PA protein plays an important role in influenza virulence and pathogenicity.

IMPORTANCE
Highly pathogenic influenza viruses of the H5N1 subtype cause severe respiratory infections in humans, which have resulted in death in nearly two-thirds of the patients with laboratory-confirmed cases. We found that the viral PA polymerase subunit of several H5N1 viruses possesses amino acid changes that attenuate virus replication in mammalian cells (yet the H5N1 viruses possessing these mutations are highly pathogenic in mice). Specifically, we found that an arginine-to-lysine substitution at position 185 of an H5N1 virus PA protein significantly affected that virus's virulence and pathogenicity in mice. The PA protein thus plays a role in the pathogenicity of highly pathogenic H5N1 influenza viruses.
Elephant Endotheliotropic Herpesviruses EEHV1A, EEHV1B, and EEHV2 from Cases of Hemorrhagic Disease Are Highly Diverged from Other Mammalian Herpesviruses and May Form a New Subfamily
Authors: Richman Laura K. , Zong Jian-Chao , Latimer Erin M. , Lock Justin , Fleischer Robert C. , Heaggans Sarah Y. , Hayward Gary S.
Published: September 2014

A family of novel endotheliotropic herpesviruses (EEHVs) assigned to the genus
Proboscivirus
have been identified as the cause of fatal hemorrhagic disease in 70 young Asian elephants worldwide. Although EEHV cannot be grown in cell culture, we have determined a total of 378 kb of viral genomic DNA sequence directly from clinical tissue samples from six lethal cases and two survivors. Overall, the data obtained encompass 57 genes, including orthologues of 32 core genes common to all herpesviruses, 14 genes found in some other herpesviruses, plus 10 novel genes, including a single large putative transcriptional regulatory protein (ORF-L). On the basis of differences in gene content and organization plus phylogenetic analyses of conserved core proteins that have just 20% to 50% or less identity to orthologues in other herpesviruses, we propose that EEHV1A, EEHV1B, and EEHV2 could be considered a new
Deltaherpesvirinae
subfamily of mammalian herpesviruses that evolved as an intermediate branch between the
Betaherpesvirinae
and
Gammaherpesvirinae
. Unlike cytomegaloviruses, EEHV genomes encode ribonucleotide kinase B subunit (RRB), thymidine kinase (TK), and UL9-like origin binding protein (OBP) proteins and have an alphaherpesvirus-like dyad symmetry Ori-Lyt domain. They also differ from all known betaherpesviruses by having a 40-kb large-scale inversion of core gene blocks I, II, and III. EEHV1 and EEHV2 DNA differ uniformly by more than 25%, but EEHV1 clusters into two major subgroups designated EEHV1A and EEHV1B with ancient partially chimeric features. Whereas large segments are nearly identical, three nonadjacent loci totaling 15 kb diverge by between 21 and 37%. One strain of EEHV1B analyzed is interpreted to be a modern partial recombinant with EEHV1A.

IMPORTANCE
Asian elephants are an endangered species whose survival is under extreme pressure in wild range countries and whose captive breeding populations in zoos are not self-sustaining. In 1999, a novel class of herpesviruses called EEHVs was discovered. These viruses have caused a rapidly lethal hemorrhagic disease in 20% of all captive Asian elephant calves born in zoos in the United States and Europe since 1980. The disease is increasingly being recognized in Asian range countries as well. These viruses cannot be grown in cell culture, but by direct PCR DNA sequence analysis from segments totaling 15 to 30% of the genomes from blood or necropsy tissue from eight different cases, we have determined that they fall into multiple types and chimeric subtypes of a novel
Proboscivirus
genus, and we propose that they should also be classified as the first examples of a new mammalian herpesvirus subfamily named the
Deltaherpesvirinae
.
Identification of Nucleotide-Level Changes Impacting Gene Content and Genome Evolution in Orthopoxviruses
Authors: Hatcher Eneida L. , Hendrickson Robert Curtis , Lefkowitz Elliot J.
Published: September 2014

Poxviruses are composed of large double-stranded DNA (dsDNA) genomes coding for several hundred genes whose variation has supported virus adaptation to a wide variety of hosts over their long evolutionary history. Comparative genomics has suggested that the
Orthopoxvirus
genus in particular has undergone reductive evolution, with the most recent common ancestor likely possessing a gene complement consisting of all genes present in any existing modern-day orthopoxvirus species, similar to the current
Cowpox virus
species. As orthopoxviruses adapt to new environments, the selection pressure on individual genes may be altered, driving sequence divergence and possible loss of function. This is evidenced by accumulation of mutations and loss of protein-coding open reading frames (ORFs) that progress from individual missense mutations to gene truncation through the introduction of early stop mutations (ESMs), gene fragmentation, and in some cases, a total loss of the ORF. In this study, we have constructed a whole-genome alignment for representative isolates from each
Orthopoxvirus
species and used it to identify the nucleotide-level changes that have led to gene content variation. By identifying the changes that have led to ESMs, we were able to determine that short indels were the major cause of gene truncations and that the genome length is inversely proportional to the number of ESMs present. We also identified the number and types of protein functional motifs still present in truncated genes to assess their functional significance.

IMPORTANCE
This work contributes to our understanding of reductive evolution in poxviruses by identifying genomic remnants such as single nucleotide polymorphisms (SNPs) and indels left behind by evolutionary processes. Our comprehensive analysis of the genomic changes leading to gene truncation and fragmentation was able to detect some of the remnants of these evolutionary processes still present in orthopoxvirus genomes and suggests that these viruses are under continual adaptation due to changes in their environment. These results further our understanding of the evolutionary mechanisms that drive virus variation, allowing orthopoxviruses to adapt to particular environmental niches. Understanding the evolutionary history of these virus pathogens may help predict their future evolutionary potential.
DDX3 DEAD-Box RNA Helicase Is a Host Factor That Restricts Hepatitis B Virus Replication at the Transcriptional Level
Authors: Ko Chunkyu , Lee Sooyoung , Windisch Marc P. , Ryu Wang-Shick
Published: September 2014

DDX3 is a member of the DEAD-box RNA helicase family, involved in mRNA metabolism, including transcription, splicing, and translation. We previously identified DDX3 as a hepatitis B virus (HBV) polymerase (Pol) binding protein, and by using a transient transfection, we found that DDX3 inhibits HBV replication at the posttranscriptional level, perhaps following encapsidation. To determine the exact mechanism of the inhibition, we here employed a diverse HBV experimental system. Inconsistently, we found that DDX3-mediated inhibition occurs at the level of transcription. By using tetracycline-inducible HBV-producing cells, we observed that lentivirus-mediated DDX3 expression led to a reduced level of HBV RNAs. Importantly, knockdown of DDX3 by short hairpin RNA resulted in augmentation of HBV RNAs in two distinct HBV replication systems: (i) tetracycline-inducible HBV-producing cells and (ii) constitutive HBV-producing HepG2.2.15 cells. Moreover, DDX3 knockdown in HBV-susceptible HepG2-NTCP cells, where covalently closed circular DNA (cccDNA) serves as the template for viral transcription, resulted in increased HBV RNAs, validating that transcription regulation by DDX3 occurs on a physiological template. Overall, our results demonstrate that DDX3 represents an intrinsic host antiviral factor that restricts HBV transcription.

IMPORTANCE
Upon entry into host cells, viruses encounter host factors that restrict viral infection. During evolution, viruses have acquired the ability to subvert cellular factors that adversely affect their replication. Such host factors include TRIM5α and APOBEC3G, which were discovered in retroviruses. The discovery of host restriction factors provided deeper insight into the innate immune response and viral pathogenesis, leading to better understanding of host-virus interactions. In contrast to the case with retroviruses, little is known about host factors that restrict hepatitis B virus (HBV), a virus distantly related to retroviruses. DDX3 DEAD box RNA helicase is best characterized as an RNA helicase involved in RNA metabolism, such as RNA processing and translation. Here, we show that DDX3 inhibits HBV infection at the level of viral transcription.
Drift of the HIV-1 Envelope Glycoprotein gp120 toward Increased Neutralization Resistance over the Course of the Epidemic: a Comprehensive Study Using the Most Potent and Broadly Neutralizing Monoclonal Antibodies
Authors: Bouvin-Pley M. , Morgand M. , Meyer L. , Goujard C. , Moreau A. , Mouquet H. , Nussenzweig M. , Pace C. , Ho D. , Bjorkman P. J. , Baty D. , Chames P. , Pancera M. , Kwong P. D. , Poignard P. , Barin F. , Braibant M.
Published: September 2014

Extending our previous analyses to the most recently described monoclonal broadly neutralizing antibodies (bNAbs), we confirmed a drift of HIV-1 clade B variants over 2 decades toward higher resistance to bNAbs targeting almost all the identified gp120-neutralizing epitopes. In contrast, the sensitivity to bNAbs targeting the gp41 membrane-proximal external region remained stable, suggesting a selective pressure on gp120 preferentially. Despite this evolution, selected combinations of bNAbs remain capable of neutralizing efficiently most of the circulating variants.
The Conserved Disulfide Bond within Domain II of Epstein-Barr Virus gH Has Divergent Roles in Membrane Fusion with Epithelial Cells and B Cells
Authors: Möhl Britta S. , Sathiyamoorthy Karthik , Jardetzky Theodore S. , Longnecker Richard
Published: September 2014

Epstein-Barr virus (EBV) infects target cells via fusion with cellular membranes. For entry into epithelial cells, EBV requires the herpesvirus conserved core fusion machinery, composed of glycoprotein B (gB) and gH/gL. In contrast, for B cell fusion it requires gB and gH/gL with gp42 serving as a cell tropism switch. The available crystal structures for gH/gL allow the targeted analysis of structural determinants of gH to identify functional regions critical for membrane fusion. Domain II of EBV gH contains two disulfide bonds (DBs). The first is unique for EBV and closely related gammaherpesviruses. The second is conserved across the beta- and gammaherpesviruses and is positioned to stabilize a putative syntaxin-like bundle motif. To analyze the role of these DBs in membrane fusion, gH was mutated by amino acid substitution of the DB cysteines. Mutation of the EBV-specific DB resulted in diminished gH/gL cell surface expression that correlated with diminished B cell and epithelial cell fusion. In contrast, mutation of the conserved DB resulted in wild-type-like B cell fusion, whereas epithelial cell fusion was greatly reduced. The gH mutants bound well to gp42 but had diminished binding to epithelial cells. Tyrosine 336, located adjacent to cysteine 335 of the conserved DB, also was found to be important for DB stabilization and gH/gL function. We conclude that the conserved DB has a cell type-specific function, since it is important for the binding of gH to epithelial cells initiating epithelial cell fusion but not for fusion with B cells and gp42 binding.

IMPORTANCE
EBV predominantly infects epithelial and B cells in humans, which can result in EBV-associated cancers, such as Burkitt and Hodgkin lymphoma, as well as nasopharyngeal carcinoma. EBV is also associated with a variety of lymphoproliferative disorders, typically of B cell origin, observed in immunosuppressed individuals, such as posttransplant or HIV/AIDS patients. The gH/gL complex plays an essential but still poorly characterized role as an important determinant for EBV cell tropism. In the current studies, we found that mutants in the DB C278/C335 and the neighboring tyrosine 336 have cell type-specific functional deficits with selective decreases in epithelial cell, but not B cell, binding and fusion. The present study brings new insights into the gH function as a determinant for epithelial cell tropism during herpesvirus-induced membrane fusion and highlights a specific gH motif required for epithelial cell fusion.
Duration and breaks in sedentary behaviour: accelerometer data from 1566 community-dwelling older men (British Regional Heart Study)
Authors: Jefferis Barbara J , Sartini Claudio , Shiroma Eric , Whincup Peter H , Wannamethee S Goya , Lee I-Min
Published: September 2014

Background

Sedentary behaviours are increasingly recognised as raising the risk of cardiovascular disease events, diabetes and mortality, independently of physical activity levels. However, little is known about patterns of sedentary behaviour in older adults.

Methods

Cross-sectional study of 1566/3137 (50% response) men aged 71–91 years from a UK population-based cohort study. Men wore a GT3x accelerometer over the hip for 1 week in 2010–2011. Mean daily minutes of sedentary behaviours, percentage of day in sedentary behaviours, sedentary bouts and breaks were calculated and summarised by health and demographic characteristics.

Results

1403 ambulatory men aged 78.4 years (SD=4.6 years) with ≥600 min of accelerometer wear on ≥3 days had complete data on covariables. Men spent on average 618 min (SD=83), or 72% of their day in sedentary behaviours (<100 counts/min). On average, men accumulated 72 spells of sedentary behaviours per day, with 7 breaks in each sedentary hour. Men had on average 5.1 sedentary bouts of ≥30 min, which accounted for 43% of sedentary time, and 1.4 bouts of ≥60 min, which accounted for 19% of daily sedentary time. Men who were over 80 years old, obese, depressed and had multiple chronic conditions accumulated more sedentary time and spent more time in longer sedentary bouts.

Conclusions

Older men spend nearly three quarters of their day in sedentary behaviours, mostly accumulated in short bouts, although bouts lasting ≥30 min accounted for nearly half of the sedentary time each day. Men with medical risk factors were more likely to also display sedentary behaviour.
Predicting risk of hospitalisation or death: a retrospective population-based analysis
Authors: Louis Daniel Z , Robeson Mary , McAna John , Maio Vittorio , Keith Scott W , Liu Mengdan , Gonnella Joseph S , Grilli Roberto
Published: September 2014

Objectives

Develop predictive models using an administrative healthcare database that provide information for Patient-Centred Medical Homes to proactively identify patients at risk of hospitalisation for conditions that may be impacted through improved patient care.

Design

Retrospective healthcare utilisation analysis with multivariate logistic regression models.

Data

A population-based longitudinal database of residents served by the Emilia-Romagna, Italy, health service in the years 2004–2012 including demographic information and utilisation of health services by 3 726 380 people aged ≥18 years.

Outcome measures

Models designed to predict risk of hospitalisation or death in 2012 for problems that are potentially avoidable were developed and evaluated using the area under the receiver operating curve C-statistic, in terms of their sensitivity, specificity and positive predictive value, and for calibration to assess performance across levels of predicted risk.

Results

Among the 3 726 380 adult residents of Emilia-Romagna at the end of 2011, 449 163 (12.1%) were hospitalised in 2012; 4.2% were hospitalised for the selected conditions or died in 2012 (3.6% hospitalised, 1.3% died). The C-statistic for predicting 2012 outcomes was 0.856. The model was well calibrated across categories of predicted risk. For those patients in the highest predicted risk decile group, the average predicted risk was 23.9% and the actual prevalence of hospitalisation or death was 24.2%.

Conclusions

We have developed a population-based model using a longitudinal administrative database that identifies the risk of hospitalisation for residents of the Emilia-Romagna region with a level of performance as high as, or higher than, similar models. The results of this model, along with profiles of patients identified as high risk are being provided to the physicians and other healthcare professionals associated with the Patient Centred Medical Homes to aid in planning for care management and interventions that may reduce their patients’ likelihood of a preventable, high-cost hospitalisation.