bluuebunny/crossref_metadata_2025 huggingface dataset:
On the Mathematical Modelling of EPS Production by a Thermophilic Bacterium
Authors: Radchenkova Nadja , Kambourova Margarita , Vassilev Spasen , Alt Rene , Markov Svetoslav
Published: July 2014

This paper presents experimental data coming from a batch fermentation process and theoretical models aiming to explain various aspects of these data. The studied process is the production of exopolysaccharides (EPS) by a thermophilic bacterium, Aeribacillus pallidus 418, isolated from the Rupi basin in South-West Bulgaria. The modelling approach chosen here is: first, biochemical reaction schemes are formulated, comprising several reaction steps; then the reaction schemes are translated into systems of ordinary differential equations (ODE) using the mass action law; then the ODE systems are studied by means of numerical simulations. The latter means that the ODE systems are parametrically identified in order to possibly fit the experimental data. A main peculiarity of the proposed reaction schemes, resp. models, is the assumption that the cell biomass consist of two dynamically interacting cell fractions (dividing and non-dividing cells). This assumption allows us to implement certain modelling ideas borrowed from enzyme kinetics. The proposed models are compared to a classical model used as reference. It is demonstrated that the introduction of the two cell fractions allows a much better fit of the experimental data. Moreover, our modelling approach allows to draw conclusions about the underlying biological mechanisms, formulating the latter in the form of simple biochemical reaction steps.
Experimental and Numerical Evaluation of Small-Scale Cryosurgery Using Ultrafine Cryoprobe
Authors: Okajima Junnosuke , Komiya Atsuki , Maruyama Shigenao
Published: July 2014

The objective of this work is to experimentally and numerically evaluate small-scale cryosurgery using an ultrafine cryoprobe. The outer diameter (OD) of the cryoprobe was 550 μm. The cooling performance of the cryoprobe was tested with a freezing experiment using hydrogel at 37 °C. As a result of 1 min of cooling, the surface temperature of the cryoprobe reached −35 °C and the radius of the frozen region was 2 mm. To evaluate the temperature distribution, a numerical simulation was conducted. The temperature distribution in the frozen region and the heat transfer coefficient was discussed.
Atomic layer deposited lithium aluminum oxide: (In)dependency of film properties from pulsing sequence
Authors: Miikkulainen Ville , Nilsen Ola , Li Han , King Sean W. , Laitinen Mikko , Sajavaara Timo , Fjellvåg Helmer
Published: July 2014

Atomic layer deposition (ALD) holds markedly high potential of becoming the enabling method for achieving the three-dimensional all-solid-state thin-film lithium ion battery (LiB). One of the most crucial components in such a battery is the electrolyte that needs to hold both low electronic conductivity and at least fair lithium ion conductivity being at the same time pinhole free. To obtain these desired properties in an electrolyte film, one necessarily has to have a good control over the elemental composition of the deposited material. The present study reports on the properties of ALD lithium aluminum oxide (LixAlyOz) thin films. In addition to LiB electrolyte applications, LixAlyOz is also a candidate low dielectric constant (low-k) etch stop and diffusion barrier material in nanoelectronics applications. The LixAlyOz films were deposited employing trimethylaluminum-O3 and lithium tert-butoxide-H2O for Al2O3 and Li2O/LiOH, respectively. The composition was aimed to be controlled by varying the pulsing ratio of those two binary oxide ALD cycles. The films were characterized by several methods for composition, crystallinity and phase, electrical properties, hardness, porosity, and chemical environment. Regardless of the applied pulsing ratio of Al2O3 and Li2O/LiOH, all the studied ALD LixAlyOz films of 200 and 400 nm in thickness were polycrystalline in the orthorhombic β-LiAlO2 phase and also very similar to each other with respect to composition and other studied properties. The results are discussed in the context of both fundamental ALD chemistry and applicability of the films as thin-film LiB electrolytes and low-k etch stop and diffusion barriers.
Surface temperature: A key parameter to control the propanethiol plasma polymer chemistry
Authors: Thiry Damien , Aparicio Francisco J. , Laha Priya , Terryn Herman , Snyders Rony
Published: July 2014

In this work, the influence of the substrate temperature (Ts) on the chemical composition of propanethiol plasma polymers was investigated for a given set of plasma conditions. In a first study, a decrease in the atomic sulfur content (at. %S) with the deposition time (td) was observed. This behavior is explained by the heating of the growing film during deposition process, limiting the incorporation of stable sulfur-based molecules produced in the plasma. Experiments carried out by controlling the substrate temperature support this hypothesis. On the other hand, an empirical law relating the Ts and the at. %S was established. This allows for the formation of gradient layer presenting a heterogeneous chemical composition along the thickness, as determined by depth profile analysis combining X-ray photoelectron spectroscopy and C60 ion gun sputtering. The experimental data fit with the one predicted from our empiric description. The whole set of our results provide new insights in the relationship between the substrate temperature and the sulfur content in sulfur-based plasma polymers, essential for future developments.
Quality control procedures for dynamic treatment delivery techniques involving couch motion
Authors: Yu Victoria Y. , Fahimian Benjamin P. , Xing Lei , Hristov Dimitre H.
Published: July 2014

In this study, the authors introduce and demonstrate quality control procedures for evaluating the geometric and dosimetric fidelity of dynamic treatment delivery techniques involving treatment couch motion synchronous with gantry and multileaf collimator (MLC). Tests were designed to evaluate positional accuracy, velocity constancy and accuracy for dynamic couch motion under a realistic weight load. A test evaluating the geometric accuracy of the system in delivering treatments over complex dynamic trajectories was also devised. Custom XML scripts that control the Varian TrueBeam™ STx (Serial #3) axes in Developer Mode were written to implement the delivery sequences for the tests. Delivered dose patterns were captured with radiographic film or the electronic portal imaging device. The couch translational accuracy in dynamic treatment mode was 0.01 cm. Rotational accuracy was within 0.3°, with 0.04 cm displacement of the rotational axis. Dose intensity profiles capturing the velocity constancy and accuracy for translations and rotation exhibited standard deviation and maximum deviations below 3%. For complex delivery involving MLC and couch motions, the overall translational accuracy for reproducing programmed patterns was within 0.06 cm. The authors conclude that in Developer Mode, TrueBeam™ is capable of delivering dynamic treatment delivery techniques involving couch motion with good geometric and dosimetric fidelity.
Coherent imaging spectroscopy of a quantum many-body spin system
Authors: Senko C. , Smith J. , Richerme P. , Lee A. , Campbell W. C. , Monroe C.
Published: July 2014

Characterization of a quantum simulator

Ultracold gases can be used to simulate the behavior of more complicated systems, such as solid materials. Senko
et al.
developed a method similar to nuclear magnetic resonance that can be used to validate the properties of such simulators. They demonstrated the method on an array of interacting trapped ions that simulate magnetism. A modulated magnetic field resonantly enhanced the transfer of the population between the different configurations of the system. The authors varied the modulation frequency to measure the energy of each configuration and mapped the effective interactions.

Science
, this issue p.
430
Defaunation in the Anthropocene
Authors: Dirzo Rodolfo , Young Hillary S. , Galetti Mauro , Ceballos Gerardo , Isaac Nick J. B. , Collen Ben
Published: July 2014

We live amid a global wave of anthropogenically driven biodiversity loss: species and population extirpations and, critically, declines in local species abundance. Particularly, human impacts on animal biodiversity are an under-recognized form of global environmental change. Among terrestrial vertebrates, 322 species have become extinct since 1500, and populations of the remaining species show 25% average decline in abundance. Invertebrate patterns are equally dire: 67% of monitored populations show 45% mean abundance decline. Such animal declines will cascade onto ecosystem functioning and human well-being. Much remains unknown about this “Anthropocene defaunation”; these knowledge gaps hinder our capacity to predict and limit defaunation impacts. Clearly, however, defaunation is both a pervasive component of the planet’s sixth mass extinction and also a major driver of global ecological change.
AP2 controls clathrin polymerization with a membrane-activated switch
Authors: Kelly Bernard T. , Graham Stephen C. , Liska Nicole , Dannhauser Philip N. , Höning Stefan , Ungewickell Ernst J. , Owen David J.
Published: July 2014

A membrane-activated switch to bind clathrin

Clathrin-mediated endocytosis—the process by which cells take up nutrients and signals within clathrin-coated vesicles—is very well understood. Kelly
et al.
reveal an unanticipated layer of regulation in this process. The proteins AP2 and clathrin are the major constituents of endocytic clathrin-coated vesicles. AP2 and clathrin stick together through a clathrin-binding motif in AP2. The authors now show that AP2's clathrin-binding motif is normally buried within the core of the AP2 protein. AP2 only ejects its clathrin-binding motif and recruits clathrin if it is associated with the correct cell membrane and an endocytic cargo.

Science
, this issue p.
459
Ultraslow relaxation of confined DNA
Authors: Chemla Yann R. , Ha Taekjip
Published: July 2014

DNA dynamics in tight spaces challenge nature's nanomachines
Why are plant-pollinator networks nested?
Authors: Pawar Samraat
Published: July 2014

Mutualistic communities maximize their structural stability

[Also see Research Article by

Rohr
et al.

]
Self-control tames the coupling of reactive radicals
Authors: Lloyd-Jones Guy C. , Ball Liam T.
Published: July 2014

Iridium complexes use two points of contact to control carbon-carbon bond formation

[Also see Reports by

Tellis
et al.

and

Zuo
et al.

]
Astrocytes eyeball axonal mitochondria
Authors: Burdett Thomas C. , Freeman Marc R.
Published: July 2014

Retinal neurons transfer mitochondria to astrocytes for rapid turnover to meet energy demands
Ghosts from the past
Authors: Titley David
Published: July 2014

2014 marks the centennial of the commencement of World War I. One connection between today and that seemingly long-ago war is how we make choices when the future seems obvious only in retrospect, in what former U.S. Secretary of State George P. Shultz refers to as a world “awash in change.” Max Hastings, in
Catastrophe 1914: Europe Goes to War
, summarizes his views on how the rulers of Europe allowed World War I to start, then continue with a loss of over 8.6 million soldiers: “It is more appropriate to call them deniers, who preferred to persist with supremely dangerous policies and strategies….”
An animal-rich future
Authors: Tewksbury Joshua J. , Rogers Haldre S.
Published: July 2014

The rate at which animals are vanishing from this planet is one of the signatures of this age, as sure a sign of human dominance as our impact on Earth's nitrogen, phosphorus, and carbon cycles. This disappearance of animals from the world's ecosystems is generally a by-product of human activity, not an intentional act. Animals do matter to people, but on balance, they matter less than food, jobs, energy, money, and development. As long as we continue to view animals in ecosystems as irrelevant to these basic demands, animals will lose.
Ebola drugs still stuck in lab
Authors: Enserink Martin
Published: July 2014

Experts discussed—and rejected—bringing experimental vaccines and therapies to West Africa.
NIH institute considers broad shift to ‘people’ awards
Authors: Kaiser Jocelyn
Published: July 2014

Approach promises freedom from grant writing but could favor established researchers.
Dengue vaccine trial poses public health quandary
Authors: Normile Dennis
Published: July 2014

Experimental vaccine fell short against key strain.
The empty forest
Authors: Stokstad Erik
Published: July 2014

A beleaguered national park in Borneo hints at what can happen when animals disappear.
Hepatitis B Virus Antibody Levels 7 to 9 Years after Booster Vaccination in Alaska Native Persons
Authors: Keck James W. , Bulkow Lisa R. , Raczniak Gregory A. , Negus Susan E. , Zanis Carolyn L. , Bruce Michael G. , Spradling Philip R. , Teshale Eyasu H. , McMahon Brian J.
Published: July 2014

Hepatitis B antibody persistence was assessed in individuals who had previously received a vaccine booster. We measured hepatitis B surface antigen antibody (anti-HBs) levels 7 to 9 years post-hepatitis B booster in individuals with primary vaccination at birth. While 95 (91.3%) of 104 participants had detectable anti-HBs (minimum, 0.1 mIU/ml; maximum, 1,029 mIU/ml), only 43 (41%) had protective levels of ≥10 mIU/ml. Pre- and week 4 postbooster anti-HBs levels were significant predictors of hepatitis B immunity at follow-up (P< 0.001). Almost all participants had detectable anti-HBs 7 to 9 years after the hepatitis B vaccine booster, but less than half had levels ≥10 mIU/ml.
A New Modified Live Porcine Reproductive and Respiratory Syndrome Vaccine Improves Growth Performance in Pigs under Field Conditions
Authors: Park Changhoon , Seo Hwi Won , Kang Ikjae , Jeong Jiwoon , Choi Kyuhyung , Chae Chanhee
Published: July 2014

The change in growth performance resulting from a new modified live porcine reproductive and respiratory syndrome (PRRS) vaccine was evaluated under field conditions for registration with the government as guided by the Republic of Korea's Animal and Plant Quarantine Agency. Three farms were selected based on their history of PRRS-associated respiratory diseases. On each farm, a total of 45 3-week-old pigs were randomly allocated to one of two treatment groups, (i) vaccinated (n= 25) or (ii) control (n= 20) animals. A new modified live PRRSV vaccine increased market weight by 1.26 kg/pig (104.71 kg versus 103.45 kg;P< 0.05) and decreased mortality by 17% (1.33% versus 18.33%;P< 0.05). Pathological examination indicated that vaccination effectively reduced microscopic lung lesions compared with control animals on the 3 farms. Thus, the new modified live PRRS vaccine improved growth performance and decreased mortality and lung lesions when evaluated under field conditions.
Genome Sequencing of Mycobacterium abscessus Isolates from Patients in the United States and Comparisons to Globally Diverse Clinical Strains
Authors: Davidson Rebecca M. , Hasan Nabeeh A. , Reynolds Paul R. , Totten Sarah , Garcia Benjamin , Levin Adrah , Ramamoorthy Preveen , Heifets Leonid , Daley Charles L. , Strong Michael
Published: July 2014

Nontuberculous mycobacterial infections caused by
Mycobacterium abscessus
are responsible for a range of disease manifestations from pulmonary to skin infections and are notoriously difficult to treat, due to innate resistance to many antibiotics. Previous population studies of clinical
M. abscessus
isolates utilized multilocus sequence typing or pulsed-field gel electrophoresis, but high-resolution examinations of genetic diversity at the whole-genome level have not been well characterized, particularly among clinical isolates derived in the United States. We performed whole-genome sequencing of 11 clinical
M. abscessus
isolates derived from eight U.S. patients with pulmonary nontuberculous mycobacterial infections, compared them to 30 globally diverse clinical isolates, and investigated intrapatient genomic diversity and evolution. Phylogenomic analyses revealed a cluster of closely related U.S. and Western European M.
abscessus
subsp.
abscessus
isolates that are genetically distinct from other European isolates and all Asian isolates. Large-scale variation analyses suggested genome content differences of 0.3 to 8.3%, relative to the reference strain ATCC 19977
T
. Longitudinally sampled isolates showed very few single-nucleotide polymorphisms and correlated genomic deletion patterns, suggesting homogeneous infection populations. Our study explores the genomic diversity of clinical
M. abscessus
strains from multiple continents and provides insight into the genome plasticity of an opportunistic pathogen.
Evaluation of 16S rRNA Gene PCR Sensitivity and Specificity for Diagnosis of Prosthetic Joint Infection: a Prospective Multicenter Cross-Sectional Study
Authors: Bémer Pascale , Plouzeau Chloé , Tande Didier , Léger Julie , Giraudeau Bruno , Valentin Anne Sophie , Jolivet-Gougeon Anne , Vincent Pascal , Corvec Stéphane , Gibaud Sophie , Juvin Marie Emmanuelle , Héry-Arnaud Genevieve , Lemarié Carole , Kempf Marie , Bret Laurent , Quentin Roland , Coffre Carine , de Pinieux Gonzague , Bernard Louis , Burucoa Christophe
Published: July 2014

There is no standard method for the diagnosis of prosthetic joint infection (PJI). The contribution of 16S rRNA gene PCR sequencing on a routine basis remains to be defined. We performed a prospective multicenter study to assess the contributions of 16S rRNA gene assays in PJI diagnosis. Over a 2-year period, all patients suspected to have PJIs and a few uninfected patients undergoing primary arthroplasty (control group) were included. Five perioperative samples per patient were collected for culture and 16S rRNA gene PCR sequencing and one for histological examination. Three multicenter quality control assays were performed with both DNA extracts and crushed samples. The diagnosis of PJI was based on clinical, bacteriological, and histological criteria, according to Infectious Diseases Society of America guidelines. A molecular diagnosis was modeled on the bacteriological criterion (≥1 positive sample for strict pathogens and ≥2 for commensal skin flora). Molecular data were analyzed according to the diagnosis of PJI. Between December 2010 and March 2012, 264 suspected cases of PJI and 35 control cases were included. PJI was confirmed in 215/264 suspected cases, 192 (89%) with a bacteriological criterion. The PJIs were monomicrobial (163 cases [85%]; staphylococci,
n
= 108; streptococci,
n
= 22; Gram-negative bacilli,
n
= 16; anaerobes,
n
= 13; others,
n
= 4) or polymicrobial (29 cases [15%]). The molecular diagnosis was positive in 151/215 confirmed cases of PJI (143 cases with bacteriological PJI documentation and 8 treated cases without bacteriological documentation) and in 2/49 cases without confirmed PJI (sensitivity, 73.3%; specificity, 95.5%). The 16S rRNA gene PCR assay showed a lack of sensitivity in the diagnosis of PJI on a multicenter routine basis.
Interspecies Transfer of
bla
IMP-4
in a Patient with Prolonged Colonization by IMP-4-Producing Enterobacteriaceae
Authors: Sidjabat Hanna E. , Heney Claire , George Narelle M. , Nimmo Graeme R. , Paterson David L.
Published: July 2014

A patient was colonized by IMP-4-producing
Enterobacter cloacae
and
Escherichia coli
strains for 7 months. IMP-4-producing
E. cloacae
strains were first and last isolated at day 33 and at 8 months after admission, respectively. IMP-4-producing
E. coli
strains were first and last isolated at days 88 and 181 after admission, respectively. The
E. cloacae
and
E. coli
isolates shared identical genetic features in terms of
bla
IMP-4
,
bla
TEM-1
,
qnrB2
,
aacA4
, HI2 plasmids, and IS
CR1
. This study shows the first prolonged colonization with
in vivo
interspecies transfer of
bla
IMP-4
.
Molecular Characterization of a Lizard Adenovirus Reveals the First Atadenovirus with Two Fiber Genes and the First Adenovirus with Either One Short or Three Long Fibers per Penton
Authors: Pénzes Judit J. , Menéndez-Conejero Rosa , Condezo Gabriela N. , Ball Inna , Papp Tibor , Doszpoly Andor , Paradela Alberto , Pérez-Berná Ana J. , López-Sanz María , Nguyen Thanh H. , van Raaij Mark J. , Marschang Rachel E. , Harrach Balázs , Benkő Mária , San Martín Carmen
Published: July 2014

Although adenoviruses (AdVs) have been found in a wide variety of reptiles, including numerous squamate species, turtles, and crocodiles, the number of reptilian adenovirus isolates is still scarce. The only fully sequenced reptilian adenovirus, snake adenovirus 1 (SnAdV-1), belongs to the
Atadenovirus
genus. Recently, two new atadenoviruses were isolated from a captive Gila monster (
Heloderma suspectum
) and Mexican beaded lizards (
Heloderma horridum
). Here we report the full genomic and proteomic characterization of the latter, designated lizard adenovirus 2 (LAdV-2). The double-stranded DNA (dsDNA) genome of LAdV-2 is 32,965 bp long, with an average G+C content of 44.16%. The overall arrangement and gene content of the LAdV-2 genome were largely concordant with those in other atadenoviruses, except for four novel open reading frames (ORFs) at the right end of the genome. Phylogeny reconstructions and plesiomorphic traits shared with SnAdV-1 further supported the assignment of LAdV-2 to the
Atadenovirus
genus. Surprisingly, two fiber genes were found for the first time in an atadenovirus. After optimizing the production of LAdV-2 in cell culture, we determined the protein compositions of the virions. The two fiber genes produce two fiber proteins of different sizes that are incorporated into the viral particles. Interestingly, the two different fiber proteins assemble as either one short or three long fiber projections per vertex. Stoichiometry estimations indicate that the long fiber triplet is present at only one or two vertices per virion. Neither triple fibers nor a mixed number of fibers per vertex had previously been reported for adenoviruses or any other virus.

IMPORTANCE
Here we show that a lizard adenovirus, LAdV-2, has a penton architecture never observed before. LAdV-2 expresses two fiber proteins—one short and one long. In the virion, most vertices have one short fiber, but a few of them have three long fibers attached to the same penton base. This observation raises new intriguing questions on virus structure. How can the triple fiber attach to a pentameric vertex? What determines the number and location of each vertex type in the icosahedral particle? Since fibers are responsible for primary attachment to the host, this novel architecture also suggests a novel mode of cell entry for LAdV-2. Adenoviruses have a recognized potential in nanobiomedicine, but only a few of the more than 200 types found so far in nature have been characterized in detail. Exploring the taxonomic wealth of adenoviruses should improve our chances to successfully use them as therapeutic tools.
Plasmacytoid Dendritic Cells Mediate Synergistic Effects of HIV and Lipopolysaccharide on CD27+IgD–Memory B Cell Apoptosis
Authors: Zhang Lumin , Luo Zhenwu , Sieg Scott F. , Funderburg Nicholas T. , Yu Xiaocong , Fu Pingfu , Wu Hao , Jiao Yanmei , Gao Yong , Greenspan Neil S. , Harding Clifford V. , Kilby J. Michael , Li Zihai , Lederman Michael M. , Jiang Wei
Published: July 2014

The effects of heightened microbial translocation on B cells during HIV infection are unknown. We examined thein vitroeffects of HIV and lipopolysaccharide (LPS) on apoptosis of CD27+IgD−memory B (mB) cells from healthy controls.In vivoanalysis was conducted on a cohort of 82 HIV+donors and 60 healthy controls.In vitroexposure of peripheral blood mononuclear cells (PBMCs) to LPS and HIV led to mB cell death via the Fas/Fas ligand (FasL) pathway. Plasmacytoid dendritic cells (pDCs) produced FasL in response to HIV via binding to CD4 and chemokine coreceptors. HIV and LPS increased Fas expression on mB cells in PBMCs, which was dependent on the presence of pDCs and monocytes. Furthermore, mB cells purified from PBMCs and pretreated with both HIV and LPS were more sensitive to apoptosis when cocultured with HIV-treated pDCs. Blocking the interferon receptor (IFNR) prevented HIV-stimulated FasL production in pDCs, HIV-plus-LPS-induced Fas expression, and apoptosis of mB cells.In vivoorex vivo, HIV+donors have higher levels of plasma LPS, Fas expression on mB cells, and mB cell apoptosis than controls. Correspondingly, in HIV+donors, but not in controls, a positive correlation was found between plasma FasL and HIV RNA levels and between Fas expression on mB cells and plasma LPS levels. This work reveals a novel mechanism of mB cell apoptosis mediated by LPS and HIV through the Fas/FasL pathway, with key involvement of pDCs and type I IFN, suggesting a role for microbial translocation in HIV pathogenesis.

IMPORTANCEThis study demonstrates that lipopolysaccharide (LPS) and type I interferon (IFN) play an important role in memory B cell apoptosis in HIV infection. It reveals a previously unrecognized role of microbial translocation in HIV pathogenesis.
Rational Design of Human Metapneumovirus Live Attenuated Vaccine Candidates by Inhibiting Viral mRNA Cap Methyltransferase
Authors: Zhang Yu , Wei Yongwei , Zhang Xiaodong , Cai Hui , Niewiesk Stefan , Li Jianrong
Published: July 2014

The paramyxoviruses human respiratory syncytial virus (hRSV), human metapneumovirus (hMPV), and human parainfluenza virus type 3 (hPIV3) are responsible for the majority of pediatric respiratory diseases and inflict significant economic loss, health care costs, and emotional burdens. Despite major efforts, there are no vaccines available for these viruses. The conserved region VI (CR VI) of the large (L) polymerase proteins of paramyxoviruses catalyzes methyltransferase (MTase) activities that typically methylate viral mRNAs at positions guanine N-7 (G-N-7) and ribose 2′-O. In this study, we generated a panel of recombinant hMPVs carrying mutations in the
S
-adenosylmethionine (SAM) binding site in CR VI of L protein. These recombinant viruses were specifically defective in ribose 2′-O methylation but not G-N-7 methylation and were genetically stable and highly attenuated in cell culture and viral replication in the upper and lower respiratory tracts of cotton rats. Importantly, vaccination of cotton rats with these recombinant hMPVs (rhMPVs) with defective MTases triggered a high level of neutralizing antibody, and the rats were completely protected from challenge with wild-type rhMPV. Collectively, our results indicate that (i) amino acid residues in the SAM binding site in the hMPV L protein are essential for 2′-O methylation and (ii) inhibition of mRNA cap MTase can serve as a novel target to rationally design live attenuated vaccines for hMPV and perhaps other paramyxoviruses, such as hRSV and hPIV3.

IMPORTANCE
Human paramyxoviruses, including hRSV, hMPV, and hPIV3, cause the majority of acute upper and lower respiratory tract infections in humans, particularly in infants, children, the elderly, and immunocompromised individuals. Currently, there is no licensed vaccine available. A formalin-inactivated vaccine is not suitable for these viruses because it causes enhanced lung damage upon reinfection with the same virus. A live attenuated vaccine is the most promising vaccine strategy for human paramyxoviruses. However, it remains a challenge to identify an attenuated virus strain that has an optimal balance between attenuation and immunogenicity. Using reverse genetics, we generated a panel of recombinant hMPVs that were specifically defective in ribose 2′-O methyltransferase (MTase) but not G-N-7 MTase. These MTase-defective hMPVs were genetically stable and sufficiently attenuated but retained high immunogenicity. This work highlights a critical role of 2′-O MTase in paramyxovirus replication and pathogenesis and a new avenue for the development of safe and efficacious live attenuated vaccines for hMPV and other human paramyxoviruses.
Immunodominance Changes as a Function of the Infecting Dengue Virus Serotype and Primary versus Secondary Infection
Authors: Weiskopf Daniela , Angelo Michael A. , Sidney John , Peters Bjoern , Shresta Sujan , Sette Alessandro
Published: July 2014

Dengue virus (DENV) is the causative agent of dengue fever (DF). This disease can be caused by any of four DENV serotypes (DENV1 to -4) which share 67 to 75% sequence homology with one another. The effect of subsequent infections with different serotypes on the T cell repertoire is not fully understood. We utilized mice transgenic for human leukocyte antigens (HLA) lacking the alpha/beta interferon (IFN-α/β) receptor to study responses to heterologous DENV infection. First, we defined the primary T cell response to DENV3 in the context of a wide range of HLA molecules. The primary DENV3 immune response recognized epitopes derived from all 10 DENV proteins, with a significant fraction of the response specific for structural proteins. This is in contrast to primary DENV2 infection, in which structural proteins are a minor component of the response, suggesting differential antigen immunodominance as a function of the infecting serotype. We next investigated the effect of secondary heterologous DENV infection on the T cell repertoire. In the case of both DENV2/3 and DENV3/2 heterologous infections, recognition of conserved/cross-reactive epitopes was either constant or expanded compared to that in homologous infection. Furthermore, in heterologous infection, previous infection with a different serotype impaired the development of responses directed to serotype-specific but not conserved epitopes. Thus, a detrimental effect of previous heterotypic responses might not be due to dysfunctional and weakly cross-reactive epitopes dominating the response. Rather, responses to the original serotype might limit the magnitude of responses directed against epitopes that are either cross-reactive to or specific for the most recently infecting serotype.

IMPORTANCEDENV transmission occurs in more than 100 countries and is an increasing public health problem in tropical and subtropical regions. At present, no effective antiviral therapy or licensed vaccine exists, and treatment is largely supportive in nature. Disease can be caused by any of the four DENV serotypes (DENV1 to -4), which share a high degree of sequence homology with one another. In this study, we have addressed the question of how the T cell repertoire changes as a function of infections with different serotypes and of subsequent heterologous secondary infections. This is of particular interest in the field of dengue viruses, in which secondary infections with different DENV serotypes increase the risk of severe disease. Our results on the evolution of the immune response after primary and secondary infections provide new insights into HLA-restricted T cell responses against DENV relevant for the design of a vaccine against DENV.
Contribution of Silent Mutations to Thermal Adaptation of RNA Bacteriophage Qβ
Authors: Kashiwagi Akiko , Sugawara Ryu , Sano Tsushima Fumie , Kumagai Tomofumi , Yomo Tetsuya
Published: July 2014

Changes in protein function and other biological properties, such as RNA structure, are crucial for adaptation of organisms to novel or inhibitory environments. To investigate how mutations that do not alter amino acid sequence may be positively selected, we performed a thermal adaptation experiment using the single-stranded RNA bacteriophage Qβ in which the culture temperature was increased from 37.2°C to 41.2°C and finally to an inhibitory temperature of 43.6°C in a stepwise manner in three independent lines. Whole-genome analysis revealed 31 mutations, including 14 mutations that did not result in amino acid sequence alterations, in this thermal adaptation. Eight of the 31 mutations were observed in all three lines. Reconstruction and fitness analyses of Qβ strains containing only mutations observed in all three lines indicated that five mutations that did not result in amino acid sequence changes but increased the amplification ratio appeared in the course of adaptation to growth at 41.2°C. Moreover, these mutations provided a suitable genetic background for subsequent mutations, altering the fitness contribution from deleterious to beneficial. These results clearly showed that mutations that do not alter the amino acid sequence play important roles in adaptation of this single-stranded RNA virus to elevated temperature.

IMPORTANCE
Recent studies using whole-genome analysis technology suggested the importance of mutations that do not alter the amino acid sequence for adaptation of organisms to novel environmental conditions. It is necessary to investigate how these mutations may be positively selected and to determine to what degree such mutations that do not alter amino acid sequences contribute to adaptive evolution. Here, we report the roles of these silent mutations in thermal adaptation of RNA bacteriophage Qβ based on experimental evolution during which Qβ showed adaptation to growth at an inhibitory temperature. Intriguingly, four synonymous mutations and one mutation in the untranslated region that spread widely in the Qβ population during the adaptation process at moderately high temperature provided a suitable genetic background to alter the fitness contribution of subsequent mutations from deleterious to beneficial at a higher temperature.
Deep Sequencing of Norovirus Genomes Defines Evolutionary Patterns in an Urban Tropical Setting
Authors: Cotten Matthew , Petrova Velislava , Phan My V. T. , Rabaa Maia A. , Watson Simon J. , Ong Swee Hoe , Kellam Paul , Baker Stephen
Published: July 2014

Norovirus is a highly transmissible infectious agent that causes epidemic gastroenteritis in susceptible children and adults. Norovirus infections can be severe and can be initiated from an exceptionally small number of viral particles. Detailed genome sequence data are useful for tracking norovirus transmission and evolution. To address this need, we have developed a whole-genome deep-sequencing method that generates entire genome sequences from small amounts of clinical specimens. This novel approach employs an algorithm for reverse transcription and PCR amplification primer design using all of the publically available norovirus sequence data. Deep sequencing and
de novo
assembly were used to generate norovirus genomes from a large set of diarrheal patients attending three hospitals in Ho Chi Minh City, Vietnam, over a 2.5-year period. Positive-selection analysis and direct examination of protein changes in the virus over time identified codons in the regions encoding proteins VP1, p48 (NS1-2), and p22 (NS4) under positive selection and expands the known targets of norovirus evolutionary pressure.

IMPORTANCE
The high transmissibility and rapid evolutionary rate of norovirus, combined with a short-lived host immune responses, are thought to be the reasons why the virus causes the majority of pediatric viral diarrhea cases. The evolutionary patterns of this RNA virus have been described in detail for only a portion of the virus genome and never for a virus from a detailed urban tropical setting. We provide a detailed sequence description of the noroviruses circulating in three Ho Chi Minh City hospitals over a 2.5-year period. This study identified patterns of virus change in known sites of host immune response and identified three additional regions of the virus genome under selection that were not previously recognized. In addition, the method described here provides a robust full-genome sequencing platform for community-based virus surveillance.
HIV-1 Infection Leads to Increased Transcription of Human Endogenous Retrovirus HERV-K (HML-2) ProvirusesIn Vivobut Not to Increased Virion Production
Authors: Bhardwaj Neeru , Maldarelli Frank , Mellors John , Coffin John M.
Published: July 2014

Recent studies suggest that human endogenous retrovirus group K (HERV-K) provirus expression plays a role in the pathogenesis of HIV-1 infection. In particular, RNA from the HML-2 subgroup of HERV-K proviruses has been reported to be highly expressed at the cellular level and detectable in the plasma of HIV-1-infected patients, suggestive of virion production and, perhaps, replication. In this study, we developed an HML-2-specific quantitative-PCR assay that detects 51 of the 89 known HML-2 proviruses in the human genome. Plasma and peripheral blood mononuclear cells (PBMCs) from HIV-negative controls and HIV-1-infected patients were collected for analysis of HML-2 RNA expression. Contrary to previous reports, we did not detect high levels of HML-2 RNA in the plasma of HIV-1-infected patients, but we did observe a significant increase of HML-2 RNA in total PBMCs compared to HIV-negative controls. The level of HML-2 expression in PBMCs does not appear to be related to patient use of antiretrovirals or to HIV-1 plasma RNA, cellular RNA, or cellular DNA levels. To investigate the source of HML-2 RNA expression, patient PBMCs were sorted into CD3+CD4+, CD3+CD8+, CD3−CD14+, and CD3−CD20+cell subsets and then analyzed for HML-2 RNA levels. No single cell subset was enriched for HML-2 RNA expression in HIV-1-infected patients, but there appears to be substantial variability in the level of HML-2 expression depending on the cell type.

IMPORTANCEHere, we report that human endogenous retrovirus group K (HERV-K) (HML-2) proviruses are expressed at significantly higher levels in peripheral blood mononuclear cells (PBMCs) from patients with HIV-1 infection than in those from uninfected individuals. However, contrary to previous reports, this expression did not lead to detectable virions in the plasma of these patients. In addition, we found that HML-2 proviruses were expressed in multiple blood cell types from HIV-1-infected individuals, and the magnitude of HML-2 expression was not related to HIV-1 disease markers in this patient cohort. These findings may have implications for HML-2-based therapies targeting HIV-1 infection.
Stability Determinants of Murine Cytomegalovirus Long Noncoding RNA7.2
Authors: Schwarz Toni M. , Kulesza Caroline A.
Published: July 2014

Cytomegalovirus is a ubiquitous herpesvirus that persistently replicates in glandular epithelial tissue. Murine cytomegalovirus expresses a 7.2-kb-long noncoding RNA (RNA7.2) that is a determinant of viral persistence in the salivary gland. RNA7.2 is an extremely long-lived intron, yet the basis of its stability is unknown. We present data that localize key sequence determinants of RNA stability to the 3′ end of RNA7.2 and suggest that stability is a result of sustained lariat conformation.
Inhibition of Phosphorylated-STAT1 Nuclear Translocation and Antiviral Protein Expression in Human Brain Vascular Adventitial Fibroblasts Infected with Varicella-Zoster Virus
Authors: Nagel Maria A. , James Stephanie F. , Traktinskiy Igor , Wyborny Ann , Choe Alexander , Rempel April , Baird Nicholas L. , Gilden Don
Published: July 2014

In varicella-zoster virus (VZV)-infected primary human brain vascular adventitial fibroblasts (BRAFs), levels of beta interferon (IFN-β,) STAT1, and STAT2 transcripts as well as STAT1 and STAT2 protein were decreased. IFN-α transcript levels were increased but not secreted IFN-α protein levels. Compared to IFN-α-treated control results, in VZV-infected BRAFs, phosphorylated STAT1 did not translocate to the nucleus, resulting in impaired downstream expression of interferon-inducible antiviral Mx1. Overall, VZV interference with the type I interferon pathway may promote virus persistence in cerebral arteries.
Performance of the Medtronic Sentrino continuous glucose management (CGM) system in the cardiac intensive care unit
Authors: Kosiborod Mikhail , Gottlieb Rebecca K , Sekella Julie A , Peterman Diane , Grodzinsky Anna , Kennedy Paul , Borkon Michael A
Published: July 2014

Background

Maintaining glucose in the target range, while avoiding hypoglycemia, is challenging in critically ill patients. We investigated the performance and safety of Medtronic Sentrino, a newly developed continuous glucose management (CGM) system for critically ill adults.

Methods

This was a prospective, single-center, single-arm, open-label study in adult patients with cardiac ICU admission. Sentrino subcutaneous glucose sensors were inserted into patients’ thigh with planned study participation of 72 h. Sensor glucose results were displayed, and the system's alerts and alarms fully enabled. Reference blood glucose was collected from central venous catheter and analyzed with a blood gas analyzer. Treatment decisions were made independently of sensor glucose values, according to the existing standard of care.

Results

A total of 21 patients were enrolled; all successfully completed the study. Sensor glucose values were displayed 96% of the time, and 870 paired blood glucose–sensor glucose points were analyzed. Overall mean absolute relative difference (MARD) was 12.8% (95% CI 11.9% to 13.6%). No clinically significant differences in accuracy were seen within subgroups of hemodynamic status (MARD 12.3% and 13.1% for compromised vs stable hemodynamics). Consensus grid analysis showed >99% of sensor glucose values within A/B zones. No device or study-related adverse events were reported. 100% of clinicians found Sentrino easy to use after two patients.

Conclusions

In our single-center experience, Sentrino CGM system demonstrated good accuracy and reliability, with no device-related adverse events in critically ill cardiac patients, and was easy to use and integrate in the cardiac ICU.

Trial registration number

NCT01763567.
Association of napping and night-time sleep with impaired glucose regulation, insulin resistance and glycated haemoglobin in Chinese middle-aged adults with no diabetes: a cross-sectional study
Authors: Baoying Huang , Hongjie Chen , Changsheng Qiu , Peijian Wu , Qingfei Lin , Yinghua Lin , Huibin Huang , Jixing Liang , Liantao Li , Ling Chen , Kaka Tang , Zichun Chen , Lixiang Lin , Jieli Lu , Yufang Bi , Guang Ning , Penli Zhu , Junping Wen , Gang Chen
Published: July 2014

Objective

To assess associations between napping and night-time sleep duration with impaired glucose regulation, insulin resistance (IR) and glycated haemoglobin (HbA1c).

Design

Cross-sectional study.

Setting

Fujian Province, China, from June 2011 to January 2012.

Participants

This study enrolled 9028 participants aged 40–65 years. Data of 7568 participants with no diabetes were included for analysis. Type 2 diabetes was defined applying WHO criteria.

Outcome measures

Participants’ daytime napping and night-time sleep duration data were collected using a standardised self-reported Chinese-language questionnaire about sleep frequency and quality. Anthropometric and laboratory parameters were also measured. IR was defined as a HOMA-IR index value >2.50. ORs and 95% CIs were derived from multivariate logistic regression models.

Results

Participants (mean age 51.1±7.0 years) included 3060 males and 4508 females with average night-time sleep of 7.9 h. A higher proportion of males napped than females. After adjustment for potential confounders, ORs for HbA1c >6.0% were 1.28 and 1.26 for those napping ≤1 h and >1 h (p=0.002 and p=0.018), respectively. Statistically significant differences in IR between nappers and non-nappers were only marginal clinically. Odds for HbA1c >6.0% were significantly lower in participants with longer night-time sleep durations than in the reference group (>8 h vs 6–8 h). Odds for IR were significantly lower in participants whose night-time sleep hours deviated from the reference group (<6 h, >8 h vs 6–8 h)

Conclusions

Chinese middle-aged adults with no diabetes who napped had higher HbA1c and IR; those with shorter night-time sleep durations had increased HbA1c. Night-time sleep hours that are either <6 or >8 tend to be associated with lower odds for IR. Further studies are necessary to determine the underlying clinical significance and mechanisms behind these associations.
The Sight Loss and Vision Priority Setting Partnership (SLV-PSP): overview and results of the research prioritisation survey process
Authors: Rowe Fiona , Wormald Richard , Cable Richard , Acton Michele , Bonstein Karen , Bowen Michael , Bronze Carol , Bunce Catey , Conroy Dolores , Cowan Katherine , Evans Kathy , Fenton Mark , Giles Heather , Gordon Iris , Halfhide Louise , Harper Robert , Lightstone Anita , Votruba Marcela , Waterman Heather , Zekite Antra
Published: July 2014

Objectives

The Sight Loss and Vision Priority Setting Partnership aimed to identify research priorities relating to sight loss and vision through consultation with patients, carers and clinicians. These priorities can be used to inform funding bodies’ decisions and enhance the case for additional research funding.

Design

Prospective survey with support from the James Lind Alliance.

Setting

UK-wide National Health Service (NHS) and non-NHS.

Participants

Patients, carers and eye health professionals. Academic researchers were excluded solely from the prioritisation process. The survey was disseminated by patient groups, professional bodies, at conferences and through the media, and was available for completion online, by phone, by post and by alternative formats (Braille and audio).

Outcome measure

People were asked to submit the questions about prevention, diagnosis and treatment of sight loss and eye conditions that they most wanted to see answered by research. Returned survey questions were reviewed by a data assessment group. Priorities were established across eye disease categories at final workshops.

Results

2220 people responded generating 4461 submissions. Sixty-five per cent of respondents had sight loss and/or an eye condition. Following initial data analysis, 686 submissions remained which were circulated for interim prioritisation (excluding cataract and ocular cancer questions) to 446 patients/carers and 218 professionals. The remaining 346 questions were discussed at final prioritisation workshops to reach agreement of top questions per category.

Conclusions

The exercise engaged a diverse community of stakeholders generating a wide range of conditions and research questions. Top priority questions were established across 12 eye disease categories.