bluuebunny/crossref_metadata_2025 huggingface dataset:
Numerical Investigation of Flow Separation Control of Low-Pressure High-Lift Blade With Different Grooves and Protrusions
Authors: Qu Huancheng , Li Ping , Chen Jianhui , Shen Zhongyang , Xie Yonghui , Zhang Di
Published: December 2013

The shear stress transport (SST) turbulence model and γ-Reθ transition model were employed when solving the Reynolds-averaged Navier-Stokes (RANS) equations. The flow separation in the suction side of the typical high-lift low-pressure gas turbine PakB blade was investigated. Different sets of mesh were adopted and the results of grid independence study show that the precision is maintained when the grid system of 126,780 is adopted. And the computational results were compared with the existing experimental and computational results, which indicate that the numerical method can predict the separated transition flow reliably. Different kinds of structures including V grooves and protrusions, curved grooves and protrusions, rectangular grooves and protrusions were used to passive control of the flow separation in the suction side of the PakB blade. The structures have the same locations including 65%Cax, 68%Cax and 71%Cax on the suction side of the blade as well as length and height for better comparison. All of these cases are compared with the flow of PakB cascade without control with Re = 86,000 and FSTI = 1%. The shear layer is uplifted when the flow passes the passive device. And the separation bubble inside the grooves almost occupies the whole groove space which makes the length of the separation shorter than that in the case without control. The separation inside the grooves joins into the downstream separation in the case of grooves located in 71%Cax. The flow starts to separate in the leeside of the protrusion wherever the protrusion locates. And the attachment point moves forward significantly in the comparison with the case of without control. However, it brings in more flow loss because of the protrusion’s resistance to the boundary flow. In the total pressure loss coefficient comparison with the case without control, the grooves produce less flow loss while the protrusions at all the locations bring more flow loss. The nearer the groove is away from the separation point in the case without control, the higher the efficiency could be in the view of total pressure loss coefficient. The rectangular grooves are considered as a more effective structure for the flow separation control of PakB blade. Moreover, the flow separation bubble length and the total pressure loss coefficient decrease as Reynolds number increases in the cases without control. The total pressure loss coefficient in the different Reynolds numbers cases with rectangular groove is lower than that in the cases without control and the flow control performance gets much better when Reynolds number increases.
Computational Study of Turbulent Airflow in a Full-Scale Aircraft Cabin Mockup: Part 1 — Determination of Boundary Conditions at the Outlet of Air Diffusers
Authors: Ebrahimi Khosrow , Hosni Mohammad H. , Zheng Zhongquan C.
Published: December 2013

The first step in understanding different mechanisms associated with contagious disease transmission in airliner cabins is adequately resolving the airflow field. A Computational Fluid Dynamic (CFD) approach is used to study the behavior of turbulent airflow and calculate the velocity data in a full-scale, 11-row, Boeing 767 aircraft cabin mockup. The calculated velocity data will be used later as the initial condition in tracer gas and particle dispersion simulations. Reynolds-Averaged Navier Stokes (RANS) method is employed for the airflow simulations. Based on the outcomes of our previous investigation in which the accuracy of different k-ε models were evaluated, the RNG k-ε model is used for turbulence modeling. The geometry of the cabin as well as the taken approach for mesh generation is also explained along with the adopted numerical method for solving the governing Navier-Stokes equations. Three different sizes of grids are examined for grid uncertainly analysis. The main challenge in airflow simulations is the determination of the unknown boundary condition (velocity magnitude and direction) at the outlet of the cabin air diffusers (or inlet of the aircraft cabin). To overcome this challenge, the mean velocity data measured by omni-probes located very close to the diffuser outlets are used as the first trial boundary conditions at the inlet of the cabin. Then, based on the differences between experimentally measured and steady RANS estimated velocity data at the omni-probes positions, the airflow velocity at the inlet of the cabin is modified and this procedure is repeated until the differences between the measured and calculated velocity data at omni-probe positions become negligible.
Aerodynamic Design for Wind-Lens Turbine Using Optimization Technique
Authors: Oka Nobuhito , Furukawa Masato , Yamada Kazutoyo , Kido Kota
Published: December 2013

An optimum aerodynamic design method has been developed for the new type of wind turbine called “wind-lens turbine”. The wind-lens turbine has a diffuser with brim called “wind-lens”, by which the wind concentration on the turbine rotor and the significant enhancement of the turbine output can be achieved. The present design method is based on a genetic algorithm (GA) and a quasi-three-dimensional design of turbine rotor. The quasi-three-dimensional design consists of two parts: meridional viscous flow calculation and two-dimensional blade element design. In the meridional viscous flow calculation, an axisymmetric viscous flow is numerically analyzed on a meridional plane to determine the wind flow rate through the wind-lens and the spanwise distribution of the rotor inlet flow. In the two-dimensional rotor blade element design, the turbine rotor blade profile is determined by a one-dimensional through flow modeling for the wind-lens turbine and a two-dimensional blade element theory based on the momentum theorem of the ducted turbine. In the present optimization method, the Non-dominated Sorting Genetic Algorithm II (NSGA-II) is used as evaluation and selection model. The Real-coded Ensemble Crossover (REX) is used as crossover model. The present aerodynamic design method has been applied to the coupled design of turbine rotor and wind-lens. Total performances and flow fields of the wind-lens turbines designed have been investigated by Reynolds averaged Navier-Stokes simulations, in order to verify the present design method.
Numerical Simulation of Burden Descending Behavior in Oxygen Blast Furnace
Authors: Jin Peng , Jiang Zeyi , E Dianyu , Wang Chaochao , Zhang Xinxin
Published: December 2013

In consideration of the environmental degradation and global scarcity of coking coal resource, substituting coke with coal and improving the gas utilization are the developing trends of ironmaking technology. Oxygen blast furnace, an ironmaking technology with top gas recycling, is most likely to be used in large-scale industrial manufacture considering its advantages of high productivity, high pulverized coal injection rate, low coke rate, high top gas calorific value, etc. The purpose of this paper is to make a little contribution to this technology on burden descending behavior in the metallurgical process. The results would provide reference for the design and operation of oxygen blast furnace. In the complex metallurgical processes with countercurrent multi-phase reactions, solid material motion plays important roles in the process since it determines the path and the residence time of the solid reactants as well as the stress distribution. The continuum model is often employed in the kinetic process analysis for its simplicity and low computational load. In this study, a viscous flow model based on the Navier-Stokes equation was developed to investigate the behavior of solid flow in oxygen blast furnace. A three dimensional experimental apparatus was constructed to observe burden descending behavior. According to concerned experimental results, it show that the interaction between the burden and the wall is not significant in shaft zone of the furnace. The descending burden maintains initial pattern until it reaches the lower part where the size of the cross section starts to reduce and the strong friction appears obviously in the tracked materials. Consequently, slip boundary condition with the Fanning equation was used for computations to describe the friction between solid flow and the wall or the dead zone. In addition, the position and the gas flow rate of the upper tuyeres were investigated. It was demonstrated that if the upper tuyeres are higher than the top of the belly, the position will strongly influence the solid flow distribution. Thus, gas velocity must be limited in a proper range to keep the solid flow falling down smoothly. By analysis of various solid viscosities, it is shown that solid flow patterns are not sensitive to solid viscosity within certain range.
Electrothermal Fluidized Bed Furnace for Thermal Treatment of Recycled Battery Wastes
Authors: Gubynskyi Mykhailo V. , Barsukov Igor V. , Gogotsi Oleksiy G. , Fedorov Sergiy S. , Livitan Mykola V. , Rohatgi Upendra
Published: December 2013

An innovative technology for processing selected recycled battery wastes from large format automotive lithium-ion batteries has been developed. One of the key steps of refining process is application of thermal treatment of granular matter in a new and improved modified electrothermal fluidized bed reactor at high temperature. The reactor design is based on fluidization and increase in electric resistance leading to higher temperatiures.
Cryptic Variation in Morphological Evolution: HSP90 as a Capacitor for Loss of Eyes in Cavefish
Authors: Rohner Nicolas , Jarosz Dan F. , Kowalko Johanna E. , Yoshizawa Masato , Jeffery William R. , Borowsky Richard L. , Lindquist Susan , Tabin Clifford J.
Published: December 2013

Eye to Eyeless

To what extent does adaptation rely on de novo mutation, as opposed to preexisting variation? It has been proposed that heat shock protein 90 (HSP90) can act to maintain cryptic variation by correcting misfolded proteins, until the system is taxed under stress conditions. Focusing on the cavefish
Astyanax mexicanus
,

Rohner
et al.

(p.
1372
) provide evidence that this mechanism contributed to morphological evolution in a natural setting where cryptic variation in eye size was masked by HSP90 in the ancestral river but revealed when the fish were reared and selected in caves.
The Genome of the Ctenophore
Mnemiopsis leidyi
and Its Implications for Cell Type Evolution
Authors: Ryan Joseph F. , Pang Kevin , Schnitzler Christine E. , Nguyen Anh-Dao , Moreland R. Travis , Simmons David K. , Koch Bernard J. , Francis Warren R. , Havlak Paul ,   NISC Comparative Sequencing Program, Smith Stephen A. , Putnam Nicholas H. , Haddock Steven H. D. , Dunn Casey W. , Wolfsberg Tyra G. , Mullikin James C. , Martindale Mark Q. , Baxevanis Andreas D.
Published: December 2013

The Base of the Animal Tree?

The identity of the most basal lineages of the animal kingdom evolutionary tree has long been contested.

Ryan
et al.

(p.
10.1126/science.1242592
; see the Perspective by

Rokas

) sequenced the genome of the ctenophore the warty comb jelly or sea walnut,
Mnemiopsis leidyi
, and conclude that ctenophores alone, not sponges or the clade consisting of both ctenophores and cnidarians, are the most basal extant animals. The results suggest a specific evolutionary process that likely occurred—including repeated gains and loss of mesoderm, expansion of genes associated with the cell cycle, growth signaling, apoptosis, and epithelial and neural cell types. Furthermore, previous hypotheses regarding the evolution of animals may require re-evaluation.
Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution
Authors: Stergachis Andrew B. , Haugen Eric , Shafer Anthony , Fu Wenqing , Vernot Benjamin , Reynolds Alex , Raubitschek Anthony , Ziegler Steven , LeProust Emily M. , Akey Joshua M. , Stamatoyannopoulos John A.
Published: December 2013

Transcription Factor Binding Sites

Transcription factors (TFs) are proteins that bind to DNA to control gene transcription.

Stergachis
et al.

(p.
1367
; see the Perspective by

Weatheritt and Babu

) examined TF binding within the human genome in more than 80 cell types. Nearly 15% of coding regions simultaneously specify both amino acid sequence and TF recognition sites. The distribution of the TF binding sites evolutionarily constrains how codons within these regions can change, independent of encoded protein function. Thus, TF binding may represent a widespread and strong evolutionary force in coding regions.
Fear Learning Enhances Neural Responses to Threat-Predictive Sensory Stimuli
Authors: Kass Marley D. , Rosenthal Michelle C. , Pottackal Joseph , McGann John P.
Published: December 2013

Fear Factor

It has generally been assumed that the most basic aspects of peripheral sensory processing do not change even if they are paired with reward or punishment. A smell should still smell the same, a color should still look the same, and any changes observed would be likely to occur downstream of the primary sensory processing areas. However, using longitudinal in vivo neurophysiology in transgenic mice,

Kass
et al.

(p.
1389
) observed that neurotransmitter release from olfactory sensory neurons themselves was selectively enhanced for threat-predictive odors after fear conditioning.
Colloid Science Collides with Liquid Crystals
Authors: Abbott Nicholas L.
Published: December 2013

Dynamic interactions of a colloidal particle with a liquid crystalline solvent can cause its diffusion to deviate from classical Brownian motion.

[Also see Report by

Turiv
et al.

]
Erythropoietin Derived by Chemical Synthesis
Authors: Wang Ping , Dong Suwei , Shieh Jae-Hung , Peguero Elizabeth , Hendrickson Ronald , Moore Malcolm A. S. , Danishefsky Samuel J.
Published: December 2013

EPO via Total Synthesis

Erythropoietin (EPO) is a hormone involved in the production of red blood cells. Synthetic EPO produced via genetically engineered cell cultures is used to treat anemia and—more controversially—to boost athletic performance. EPO is a glycoprotein, and though its protein component is well-defined, both natural and synthetic EPO exhibit a wide range of attached oligosaccharides.

Wang
et al.

(p.
1357
; see the Perspective by

Hsieh-Wilson and Griffin

) prepared an EPO sample by a chemical synthesis that maintains a uniform pattern of attached sugars throughout, which may prove helpful in the analysis of how variation in the sugar components of EPO impact function.
Unnecessary Complexity

Complexity and the Arrow of Time
Charles H. Lineweaver, Paul C. W. Davies, and Michael Ruse, Eds.

Cambridge University Press, Cambridge, 2013. 369 pp. $30, £21.99. ISBN 9781107027251.
Authors: McShea Daniel W.
Published: December 2013

The contributors examine the nature of complexity and its changes over time as well as their causes.
An Enzymatic Route to H
2
Storage
Authors: Pereira Inês A. C.
Published: December 2013

An enzyme efficiently hydrogenates carbon dioxide to produce formate, a liquid that has a high energy density and can be safely transported.

[Also see Report by
Schuchmann and Müller
]
Fossilized Teeth Offer Mouthful on Ancient Microbiome
Authors: Curry Andrew
Published: December 2013

Microbial DNA preserved in ancient dental calculus—and in equally prosaic human coprolites (fossilized or preserved feces)—carries a record of the communities of bacteria that lived in and on people who died hundreds or thousands of years ago.
Development of a Recombinant Protein-Based Enzyme-Linked Immunosorbent Assay for Diagnosis of Mycoplasma bovis Infection in Cattle
Authors: Wawegama Nadeeka K. , Browning Glenn F. , Kanci Anna , Marenda Marc S. , Markham Philip F.
Published: December 2013

Mycoplasma boviscauses a range of diseases in cattle, including mastitis, arthritis, and pneumonia. However, accurate serological diagnosis of infection remains problematic. The studies described here aimed to identify an antigen that might be used to develop a more specific and sensitive diagnostic assay. A 226-kDa immunogenic protein was consistently detected in Western blots by antibodies in sera from calves experimentally infected withM. bovis. This protein was shown to be a membrane protein with lipase activity and was named mycoplasma immunogenic lipase A (MilA). Different regions of MilA were expressed inEscherichia colias glutathioneS-transferase (GST) fusion proteins and recombinant products from the amino-terminal end shown to have strong immunoreactivity withM. bovis-specific bovine sera. The most immunoreactive fusion protein, GST-MilA-ab, was used to develop indirect IgM and IgG enzyme-linked immunosorbent assays (ELISAs). The IgM ELISA detectedM. bovis-specific IgM antibody 2 weeks after infection with 97.1% sensitivity and had a specificity of 63.3%, while the IgG ELISA detectedM. bovis-specific IgG 3 weeks after infection with 92.86% sensitivity and had a specificity of 98.7%, demonstrating that the IgG ELISA has potential for use as a sensitive and specific assay for detecting infection in cattle.
Ocular Immune Responses in Steers following Intranasal Vaccination with Recombinant Moraxella bovis Cytotoxin Adjuvanted with Polyacrylic Acid
Authors: Angelos John A. , Edman Judy M. , Chigerwe Munashe
Published: December 2013

Infectious bovine keratoconjunctivitis (IBK) caused byMoraxella bovisis the most common eye disease of cattle. The pathogenesis ofM. bovisrequires the expression of pili that enable the organism to attach to the ocular surface and an RTX (repeats in the structural toxin) toxin (cytotoxin or hemolysin), which is cytotoxic to corneal epithelial cells. In this pilot study, ocular mucosal immune responses of steers were measured following intranasal (i.n.) vaccination with a recombinantM. boviscytotoxin adjuvanted with polyacrylic acid. Beef steers were vaccinated with either 500 μg (n= 3) or 200 μg (n= 3) of recombinantM. boviscytotoxin plus adjuvant. Control group steers (n= 2) were vaccinated with adjuvant alone, and all steers were given a booster on day 21. Antigen-specific tear IgA and tear IgG, tear cytotoxin-neutralizing antibody responses, and serum cytotoxin-neutralizing antibody responses were determined in samples collected prevaccination and on days 14, 28, 42, and 55. Changes in tear antigen-specific IgA levels from day 0 to days 28, 42, and 55 were significantly different between groups; however, inpost hoccomparisons between individual group pairs at the tested time points, the differences were not significant. Our results suggest that i.n. vaccination of cattle with recombinantM. boviscytotoxin adjuvanted with polyacrylic acid effects changes in ocular antigen-specific IgA concentrations. The use of intranasally administered recombinantM. boviscytotoxin adjuvanted with polyacrylic acid could provide an alternative to parenteral vaccination of cattle for immunoprophylaxis against IBK.
Colorimetric Sensor Array Allows Fast Detection and Simultaneous Identification of Sepsis-Causing Bacteria in Spiked Blood Culture
Authors: Lim Sung H. , Mix Samantha , Xu Zeyu , Taba Brian , Budvytiene Indre , Berliner Anders N. , Queralto Nuria , Churi Yair S. , Huang Richard S. , Eiden Michael , Martino Raymond A. , Rhodes Paul , Banaei Niaz
Published: December 2013

Sepsis is a medical emergency demanding early diagnosis and tailored antimicrobial therapy. Every hour of delay in initiating effective therapy measurably increases patient mortality. Blood culture is currently the reference standard for detecting bloodstream infection, a multistep process which may take one to several days. Here, we report a novel paradigm for earlier detection and the simultaneous identification of pathogens in spiked blood cultures by means of a metabolomic “fingerprint” of the volatile mixture outgassed by the organisms. The colorimetric sensor array provided significantly faster detection of positive blood cultures than a conventional blood culture system (12.1 h versus 14.9 h,P< 0.001) while allowing for the identification of 18 bacterial species with 91.9% overall accuracy within 2 h of growth detection. The colorimetric sensor array also allowed for discrimination between unrelated strains of methicillin-resistantStaphylococcus aureus, indicating that the metabolomic fingerprint has the potential to track nosocomial transmissions. Altogether, the colorimetric sensor array is a promising tool that offers a new paradigm for diagnosing bloodstream infections.
Yeast Identification Algorithm Based on Use of the Vitek MS System Selectively Supplemented with Ribosomal DNA Sequencing: Proposal of a Reference Assay for Invasive Fungal Surveillance Programs in China
Authors: Zhang Li , Xiao Meng , Wang He , Gao Ran , Fan Xin , Brown Mitchell , Gray Timothy J. , Kong Fanrong , Xu Ying-Chun
Published: December 2013

Sequence analysis of the internal transcribed spacer (ITS) region was employed as the gold standard method for yeast identification in the China Hospital Invasive Fungal Surveillance Net (CHIF-NET). It has subsequently been found that matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is potentially a more practical approach for this purpose. In the present study, the performance of the Vitek MS v2.0 system for the identification of yeast isolates collected from patients with invasive fungal infections in the 2011 CHIF-NET was evaluated. A total of 1,243 isolates representing 31 yeast species were analyzed, and the identification results by the Vitek MS v2.0 system were compared to those obtained by ITS sequence analysis. By the Vitek MS v2.0 system, 96.7% (
n
= 1,202) of the isolates were correctly assigned to the species level and 0.2% (
n
= 2) of the isolates were identified to the genus level, while 2.4% (
n
= 30) and 0.7% (
n
= 9) of the isolates were unidentified and misidentified, respectively. After retesting of the unidentified and misidentified strains, 97.3% (
n
= 1,209) of the isolates were correctly identified to the species level. Based on these results, a testing algorithm that combines the use of the Vitek MS system with selected supplementary ribosomal DNA (rDNA) sequencing was developed and validated for yeast identification purposes. By employing this algorithm, 99.7% (1,240/1,243) of the study isolates were accurately identified with the exception of two isolates of
Candida fermentati
and one isolate of
Cryptococcus gattii
. In conclusion, the proposed identification algorithm could be practically implemented in strategic programs of fungal infection surveillance.
High-Resolution Melt PCR Analysis for Genotyping of Ureaplasma parvum Isolates Directly from Clinical Samples
Authors: Payne Matthew S. , Tabone Tania , Kemp Matthew W. , Keelan Jeffrey A. , Spiller O. Brad , Newnham John P.
Published: December 2013

Ureaplasma
sp. infection in neonates and adults underlies a variety of disease pathologies. Of the two human
Ureaplasma
spp.,
Ureaplasma parvum
is clinically the most common. We have developed a high-resolution melt (HRM) PCR assay for the differentiation of the four serovars of
U. parvum
in a single step. Currently
U. parvum
strains are separated into four serovars by sequencing the promoter and coding region of the multiple-banded antigen (MBA) gene. We designed primers to conserved sequences within this region for PCR amplification and HRM analysis to generate reproducible and distinct melt profiles that distinguish clonal representatives of serovars 1, 3, 6, and 14. Furthermore, our HRM PCR assay could classify DNA extracted from 74 known (MBA-sequenced) test strains with 100% accuracy. Importantly, HRM PCR was also able to identify
U. parvum
serovars directly from 16 clinical swabs. HRM PCR performed with DNA consisting of mixtures of combined known serovars yielded profiles that were easily distinguished from those for single-serovar controls. These profiles mirrored clinical samples that contained mixed serovars. Unfortunately, melt curve analysis software is not yet robust enough to identify the composition of mixed serovar samples, only that more than one serovar is present. HRM PCR provides a single-step, rapid, cost-effective means to differentiate the four serovars of
U. parvum
that did not amplify any of the known 10 serovars of
Ureaplasma urealyticum
tested in parallel. Choice of reaction reagents was found to be crucial to allow sufficient sensitivity to differentiate
U. parvum
serovars directly from clinical swabs rather than requiring cell enrichment using microbial culture techniques.
Characterization of Human Astrovirus Cell Entry
Authors: Méndez Ernesto , Muñoz-Yañez Claudia , Sánchez-San Martín Claudia , Aguirre-Crespo Gabriela , Baños-Lara M. del Rocio , Gutierrez Michelle , Espinosa Rafaela , Acevedo Yunuén , Arias Carlos F. , López Susana
Published: December 2013

Human astroviruses (HAstV) are a frequent cause of gastroenteritis in young children and immunocompromised patients. To understand the early steps of HAstV infection in the highly permissive Caco-2 cell line, the binding and entry processes of the virus were characterized. The half-time of virus binding to the cell surface was about 10 min, while virus decapsidation took around 130 min. Drugs affecting clathrin-mediated endocytosis, endosome acidification, and actin filament polymerization, as well as those that reduce the presence of cholesterol in the cell membrane, decreased the infectivity of the virus. The infection was also reduced by silencing the expression of the clathrin heavy chain (CHC) by RNA interference or by overexpression of dominant-negative mutants of dynamin 2 and Eps15. Furthermore, the entry of HAstV apparently depends on the maturation of endosomes, since the infection was reduced by silencing the expression of Rab7, a small GTPase involved in the early- to late-endosome maturation. Altogether, our results suggest that HAstV enters Caco-2 cells using a clathrin-dependent pathway and reaches late endosomes to enter cells. Here, we have characterized the mechanism used by human astroviruses, important agents of gastroenteritis in children, to gain entry into their host cells. Using a combination of biochemical and genetic tools, we found that these viruses enter Caco-2 cells using a clathrin-dependent endocytic pathway, where they most likely need to travel to late endosomes to reach the cytoplasm and begin their replication cycle.
In Vivo
SELEX of Single-Stranded Domains in the HIV-1 Leader RNA
Authors: van Bel Nikki , Das Atze T. , Berkhout Ben
Published: December 2013

The 5′ untranslated leader region of the human immunodeficiency virus type 1 (HIV-1) RNA genome is a strongly conserved sequence that encodes several regulatory motifs important for viral replication. Most of these motifs are exposed as hairpin structures, including the dimerization initiation signal (DIS), the major splice donor site (SD), and the packaging signal (Ψ), which are connected by short single-stranded regions. Mutational analysis revealed many functions of these hairpins, but only a few studies have focused on the single-stranded purine-rich sequences. Using the
in vivo
SELEX (systematic evolution of ligands by exponential enrichment) approach, we probed the sequence space in these regions that is compatible with efficient HIV-1 replication and analyzed the impact on the RNA secondary structure of the leader RNA. Our results show a strong sequence requirement for the DIS hairpin flanking regions. We postulate that these sequences are important for the binding of specific protein factors that support leader RNA-mediated functions. The sequence between the SD and Ψ hairpins seems to have a less prominent role, despite the strong conservation of the stretch of 5 A residues in natural isolates. We hypothesize that this may reflect the subtle evolutionary pressure on HIV-1 to acquire an A-rich RNA genome.
In silico
analyses indicate that sequences are avoided in all 3 single-stranded domains that affect the local or overall leader RNA folding.

IMPORTANCE
Many regulatory RNA sequences are clustered in the untranslated leader domain of the HIV-1 RNA genome. Several RNA hairpin structures in this domain have been proposed to fulfill specific roles, e.g., mediating RNA dimer formation to facilitate HIV-1 recombination. We now focus on the importance of a few well-conserved single-stranded sequences that connect these hairpins. We created libraries of HIV-1 variants in which these segments were randomized and selected the best-replicating variants. For two segments we document the selection of the (nearly) wild-type sequence, thus demonstrating the importance of these primary nucleotide sequences and the power of the
in vivo
SELEX approach. However, for the third segment a large variety of sequences is compatible with efficient HIV-1 replication. Interestingly, the A-rich sequence of this segment is highly conserved among HIV-1 isolates, which likely reflects the evolutionary tendency of HIV-1 to adopt A-rich sequences.
Genetic Variation
In Vitro
and
In Vivo
of an Attenuated Lassa Vaccine Candidate
Authors: Zapata Juan C. , Goicochea Marco , Nadai Yuka , Eyzaguirre Lindsay M. , Carr Jean K. , Tallon Luke J. , Sadzewicz Lisa , Myers Garry , Fraser Claire M. , Su Qi , Djavani Mahmoud , Lukashevich Igor S. , Salvato Maria S.
Published: December 2013

The attenuated Lassa vaccine candidate ML29 is a laboratory-produced reassortant between Lassa and Mopeia viruses, two Old World arenaviruses that differ by 40% in nucleic acid sequence. In our previous studies, ML29 elicited sterilizing immunity against Lassa virus challenge in guinea pigs and marmosets and virus-specific cell-mediated immunity in both simian immunodeficiency virus (SIV)-infected and uninfected rhesus macaques. Here, we show that ML29 is stable after 12 passages
in vitro
without losing its plaque morphology or its attenuated phenotype in suckling mice. Additionally, we used deep sequencing to characterize the viral population comprising the original stock of ML29, the stock of ML29 after 12 passages in Vero cells, and the ML29 isolates obtained from vaccinated animals. Twenty-seven isolates bore approximately 77 mutations that exceeded 20% of the single-nucleotide polymorphism (SNP) changes at any single locus. Of these 77 mutations, 5 appeared to be host specific, for example, appearing in mice but not in primates. None of these mutations were reversions of ML29 to the sequences of the parental Lassa and Mopeia viruses. The host-specific mutations indicate viral adaptations to virus-host interactions, and such interactions make reasonable targets for antiviral approaches. Variants capable of chronic infection did not emerge from any of the primate infections, even in immune-deficient animals, indicating that the ML29 reassortant is reasonably stable
in vivo
. In conclusion, the preclinical studies of ML29 as a Lassa virus vaccine candidate have been advanced, showing high levels of protection in nonhuman primates and acceptable stability both
in vitro
and
in vivo
.
Utility of Humanized BLT Mice for Analysis of Dengue Virus Infection and Antiviral Drug Testing
Authors: Frias-Staheli Natalia , Dorner Marcus , Marukian Svetlana , Billerbeck Eva , Labitt Rachael N. , Rice Charles M. , Ploss Alexander
Published: December 2013

Dengue virus (DENV) is the cause of a potentially life-threatening disease that affects millions of people worldwide. The lack of a small animal model that mimics the symptoms of DENV infection in humans has slowed the understanding of viral pathogenesis and the development of therapies and vaccines. Here, we investigated the use of humanized “bone marrow liver thymus” (BLT) mice as a model for immunological studies and assayed their applicability for preclinical testing of antiviral compounds. Human immune system (HIS) BLT-NOD
/SCID
mice were inoculated intravenously with a low-passage, clinical isolate of DENV-2, and this resulted in sustained viremia and infection of leukocytes in lymphoid and nonlymphoid organs. In addition, DENV infection increased serum cytokine levels and elicited DENV-2-neutralizing human IgM antibodies. Following restimulation with DENV-infected dendritic cells,
in vivo
-primed T cells became activated and acquired effector function. An adenosine nucleoside inhibitor of DENV decreased the circulating viral RNA when administered simultaneously or 2 days postinfection, simulating a potential treatment protocol for DENV infection in humans. In summary, we demonstrate that BLT mice are susceptible to infection with clinical DENV isolates, mount virus-specific adaptive immune responses, and respond to antiviral drug treatment. Although additional refinements to the model are required, BLT mice are a suitable platform to study aspects of DENV infection and pathogenesis and for preclinical testing of drug and vaccine candidates.

IMPORTANCE
Infection with dengue virus remains a major medical problem. Progress in our understanding of the disease and development of therapeutics has been hampered by the scarcity of small animal models. Here, we show that humanized mice, i.e., animals engrafted with components of a human immune system, that were infected with a patient-derived dengue virus strain developed clinical symptoms of the disease and mounted virus-specific immune responses. We further show that this mouse model can be used to test preclinically the efficacy of antiviral drugs.
Unraveling the Entry Mechanism of Baculoviruses and Its Evolutionary Implications
Authors: Wang Manli , Wang Jue , Yin Feifei , Tan Ying , Deng Fei , Chen Xinwen , Jehle Johannes A. , Vlak Just M. , Hu Zhihong , Wang Hualin
Published: December 2013

The entry of baculovirus budded virus into host cells is mediated by two distinct types of envelope fusion proteins (EFPs), GP64 and F protein. Phylogenetic analysis suggested that F proteins were ancestral baculovirus EFPs, whereas GP64 was acquired by progenitor group I alphabaculovirus more recently and may have stimulated the formation of the group I lineage. This study was designed to experimentally recapitulate a possible major step in the evolution of baculoviruses. We demonstrated that the infectivity of an F-null group II alphabaculovirus (
Helicoverpa armigera
nucleopolyhedrovirus [HearNPV]) can be functionally rescued by coinsertion of GP64 along with the nonfusogenic F
def
(furin site mutated HaF) from HearNPV. Interestingly, HearNPV enters cells by endocytosis and, less efficiently, by direct membrane fusion at low pH. However, this recombinant HearNPV coexpressing F
def
and GP64 mimicked group I virus not only in its EFP composition but also in its abilities to enter host cells via low-pH-triggered direct fusion pathway. Neutralization assays indicated that the nonfusogenic F proteins contribute mainly to binding to susceptible cells, while GP64 contributes to fusion. Coinsertion of GP64 with an F-like protein (Ac23) from group I virus led to efficient rescue of an F-null group II virus. In summary, these recombinant viruses and their entry modes are considered to resemble an evolutionary event of the acquisition of GP64 by an ancestral group I virus and subsequent adaptive inactivation of the original F protein. The study described here provides the first experimental evidence to support the hypothesis of the evolution of baculovirus EFPs.
A Novel DDB2-ATM Feedback Loop Regulates Human Cytomegalovirus Replication
Authors: E Xiaofei , Savidis George , Chin Christopher R. , Wang Shixia , Lu Shan , Brass Abraham L. , Kowalik Timothy F.
Published: December 2013

Human cytomegalovirus (HCMV) genome replication requires host DNA damage responses (DDRs) and raises the possibility that DNA repair pathways may influence viral replication. We report here that a nucleotide excision repair (NER)-associated-factor is required for efficient HCMV DNA replication. Mutations in genes encoding NER factors are associated with xeroderma pigmentosum (XP). One of the XP complementation groups, XPE, involves mutation in
ddb2
, which encodes DNA damage binding protein 2 (DDB2). Infectious progeny virus production was reduced by >2 logs in XPE fibroblasts compared to levels in normal fibroblasts. The levels of immediate early (IE) (IE2), early (E) (pp65), and early/late (E/L) (gB55) proteins were decreased in XPE cells. These replication defects were rescued by infection with a retrovirus expressing DDB2 cDNA. Similar patterns of reduced viral gene expression and progeny virus production were also observed in normal fibroblasts that were depleted for DDB2 by RNA interference (RNAi). Mature replication compartments (RCs) were nearly absent in XPE cells, and there were 1.5- to 2.0-log reductions in viral DNA loads in infected XPE cells relative to those in normal fibroblasts. The expression of viral genes (
UL122
,
UL44
,
UL54
,
UL55
, and
UL84
) affected by DDB2 status was also sensitive to a viral DNA replication inhibitor, phosphonoacetic acid (PAA), suggesting that DDB2 affects gene expression upstream of or events associated with the initiation of DNA replication. Finally, a novel, infection-associated feedback loop between DDB2 and ataxia telangiectasia mutated (ATM) was observed in infected cells. Together, these results demonstrate that DDB2 and a DDB2-ATM feedback loop influence HCMV replication.
A Hypothesis for the Anti-Inflammatory and Mechanotransduction Molecular Mechanisms Underlying Acupuncture Tendon Healing
Authors: de Almeida Marcos dos Santos , Guerra Flávia Da Ré , de Oliveira Letícia Prado , Vieira Cristiano Pedrozo , Pimentel Edson Rosa
Published: December 2013

A previous study demonstrated that acupuncture increases the synthesis and reorganisation of collagen molecules in rat tendons after injury. Clinical studies have shown that acupuncture improves pain and functional activity in patients with tendinopathy. However, the molecular mechanisms underlying these effects are unknown. Recent studies have shown that acupuncture can modulate both anti-inflammatory (AI) and mechanotransduction (MT) molecular pathways. Moreover, the modulation of these pathways can increase type I collagen synthesis, which is the main factor that influences tendon biomechanical properties. Our hypothesis is that acupuncture increases synthesis and subsequent reorganisation of type I collagen during tendon healing by concomitant modulation of the Toll-like receptor-nuclear factor-κB AI pathway, the mitogen-activated protein kinases pathway and the Rho/Rac-F-actin MT pathway. Increased collagen synthesis and reorganisation requires that at least one acupoint is anatomically connected with the site of the injury because of the local tenoblast MT mechanism. Confirmation of this hypothesis will increase the knowledge of acupuncture modulation of the previously mentioned molecular pathways, and such confirmation may also help to establish the relationships between the different types of acupuncture needle stimulation and the influence of acupuncture stimuli on pathway activity levels. In addition, the downstream therapeutic effects of acupuncture therapy may be established. This hypothesis can be verified in a rat tendon healing model, and subsequent clinical protocols for tendon healing can be developed and evaluated as standalone therapies or as a component of a combination therapy.
Non-puerperal uterine inversion caused by malignant mixed mullerian sarcoma
Authors: Mehra Reeti , Siwatch Sujata , Arora Sunita , Kundu Reetu
Published: December 2013

Non puerperal uterine inversions resulting from mixed mullerian uterine sarcoma are rare. We present a case of a postmenopausal woman with a large mixed mullerian tumour presenting as a huge abdominopelvic mass. It required a challenging surgical procedure to remove the tumour which is also described along with the review of literature.
Symptomatic ureteric triplex in a child
Authors: Calvert William , Mullassery Dhanya , Kenny Simon E
Published: December 2013

We describe a case of a triplex system in a 4-year-old girl that was associated with a ureterocele and vesicoureteric reflux and causing symptomatic culture-proven urinary tract infections. Undetected on preoperative ultrasound imaging and micturating cystourethrogram, this was discovered at the time of a planned left heminephrectomy. The redundant system having been removed the patient is now asymptomatic.
Can routinely collected ambulance data about assaults contribute to reduction in community violence?
Authors: Ariel Barak , Weinborn Cristobal , Boyle Adrian
Published: December 2013

Background

The ‘law of spatiotemporal concentrations of events’ introduced major preventative shifts in policing communities. ‘Hotspots’ are at the forefront of these developments yet somewhat understudied in emergency medicine. Furthermore, little is known about interagency ‘data-crossover’, despite some developments through the Cardiff Model. Can police-ED interagency data-sharing be used to reduce community-violence using a hotspots methodology?

Methods

12-month (2012) descriptive study and analysis of spatiotemporal clusters of police and emergency calls for service using hotspots methodology and assessing the degree of incident overlap. 3775 violent crime incidents and 775 assault incidents analysed using spatiotemporal clustering withk-means++algorithm and Spearman's rho.

Results

Spatiotemporal location of calls for services to the police and the ambulance service are equally highly concentrated in a small number of geographical areas, primarily within intra-agency hotspots (33% and 53%, respectively) but across agencies’ hotspots as well (25% and 15%, respectively). Datasets are statistically correlated with one another at the 0.57 and 0.34 levels, with 50% overlap when adjusted for the number of hotspots. At least one in every two police hotspots does not have an ambulance hotspot overlapping with it, suggesting half of assault spatiotemporal concentrations are unknown to the police. Data further suggest that more severely injured patients, as estimated by transfer to hospital, tend to be injured in the places with the highest number of police-recorded crimes.

Conclusions

A hotspots approach to sharing data circumvents the problem of disclosing person-identifiable data between different agencies. Practically, at least half of ambulance hotspots are unknown to the police; if causal, it suggests that data sharing leads to both reduced community violence by way of prevention (such as through anticipatory patrols or problem-oriented policing), particularly of more severe assaults, and improved efficiency of resource deployment.
Estimating bias from loss to follow-up in a prospective cohort study of bicycle crash injuries
Authors: Tin Tin Sandar , Woodward Alistair , Ameratunga Shanthi
Published: December 2013

Background

Loss to follow-up, if related to exposures, confounders and outcomes of interest, may bias association estimates. We estimated the magnitude and direction of such bias in a prospective cohort study of crash injury among cyclists.

Methods

The Taupo Bicycle Study involved 2590 adult cyclists recruited from New Zealand's largest cycling event in 2006 and followed over a median period of 4.6 years through linkage to four administrative databases. We resurveyed the participants in 2009 and excluded three participants who died prior to the resurvey. We compared baseline characteristics and crash outcomes of the baseline (2006) and follow-up (those who responded in 2009) cohorts by ratios of relative frequencies and estimated potential bias from loss to follow-up on seven exposure-outcome associations of interest by ratios of HRs.

Results

Of the 2587 cyclists in the baseline cohort, 1526 (60%) responded to the follow-up survey. The responders were older, more educated and more socioeconomically advantaged. They were more experienced cyclists who often rode in a bunch, off-road or in the dark, but were less likely to engage in other risky cycling behaviours. Additionally, they experienced bicycle crashes more frequently during follow-up. The selection bias ranged between −10% and +9% for selected associations.

Conclusions

Loss to follow-up was differential by demographic, cycling and behavioural risk characteristics as well as crash outcomes, but did not substantially bias association estimates of primary research interest.
Correlation of thrombus formation on 7 T MRI with histology in a rat carotid artery side wall aneurysm model
Authors: Zhang Chao , Chaudhary Neeraj , Gemmete Joseph J , Elias Augusto , Song Jianping , Thompson Byron G , Galban Craig , Xi Guohua , Pandey Aditya S
Published: December 2013

Background/purpose

Various aneurysm animal models have been utilized to study the histological reaction post coil embolization. Our aim was to evaluate the imaging findings at day 14 of a rat external carotid artery side wall aneurysm treated with coil embolization using a gradient echo sequence on 7 T MRI and to correlate this with the histological findings.

Materials and methods

Male Sprague Drawley rats were utilized to create a sidewall external carotid artery blind pouch aneurysm. A 5 mm segment of hydrocoil or bare platinum coil was inserted into the created aneurysm. Five sham operated rats were used as controls. The arterial construct was harvested on day 14. The block of tissue was evaluated with histopathology and immunohistochemistry. Prior to sacrifice, the animal underwent 7 T MRI. Statistical analysis was then performed to assess the correlation of signal abnormality with intra-aneurysmal thrombus formation on histology.

Results

10 rats were used for the experiment. Five rats had implantation of hydrocoils and five of bare platinum coils. There was a statistically significant linear correlation between the intra-aneurysmal thrombus on histology and gradient echo 7 T MRI sequences. There was no correlation demonstrated in the hydrocoil implanted group. No thrombus or abnormal signal was seen in the sham group.

Conclusions

In our experiment, thrombus formation in aneurysms treated with bare platinum coils is well correlated with the presence of abnormal signal on 7 T MRI at 14 days. No correlation was appreciated in the hydrocoil implanted group due to the presence of intra-aneurysmal reactive tissue instead of thrombus.
Relationship between circadian period and body size in thetau-mutant golden hamster
Authors: Refinetti Roberto
Published: December 2013

The tau mutation in the golden (Syrian) hamster is a single gene mutation that drastically affects the speed of the circadian clock, in such a way that homozygous mutants have an endogenous circadian period of 20 h (compared with 24 h for wild-type hamsters). While studying the circadian system of tau-mutant hamsters during the past 25 years, several authors have noted an apparent relationship between circadian period and body size in these animals. This study, based on 181 hamsters from 24 litters, confirmed previous observations that a shorter circadian period is associated with smaller body size, documented a sex difference in this association, and evaluated several mechanisms that might explain the phenomenon (such as different organ sizes, body composition, and metabolic rate). The obtained evidence suggests that the reduced body size of short-period hamsters is likely a pleiotropic effect of the tau allele (an allele of the casein kinase 1 epsilon gene) rather than a consequence of the shortened circadian period.