Nonempirical Free Volume Viscosity Model for Alkane Lubricants under Severe Pressures.

Viscosities η and diffusion coefficients D_{s} of linear and branched alkanes at pressure 0

Historical Perspective of Arboviruses in Mozambique and Its Implication for Current and Future Epidemics.

Mozambique is a tropical country situated in the Southern part of Africa, a region where data on the burden and epidemiology of arbovirus is presently quite scarce although the frequency of outbreaks caused by arboviruses is rapidly increasing. Outbreaks of dengue fever have been reported in Mozambique, Angola and Tanzania and a recent unprecedented outbreak of Yellow fever has been recorded in Angola. These new outbreaks collectively suggest that arboviruses, and specifically flavivirus infections, are endemic in Mozambique.Although recent data on arbovirus activity is scarce, the work of Kokernot et al. [R.H. Kokernot, K.C. Smithburn, A.F. Gandara, B.M. Mc'Intosh and C.S. Heymann Anais Inst Med Trop (1960), 17:201-230] describes seroepidemiological and entomological studies carried out in several parts of Mozambique during the 1950s. Complementary seroepidemiological investigations on arboviruses that were conducted in the early 1980s also found serological evidence of several arboviruses which included Dengue, Chikungunya, Zika, Rift Valey Fever, Sinbdis virus, Wesselsbron, Bunyamwera, Pongola and Bawamba Fever and Yellow Fever.Notably the first description of Chikungunya virus in 1952-1953 in Tanzania also included reported cases in northern Mozambique. Furthermore, DENV serotype 3 was for the first time described in northern Mozambique in 1984 and 1985. Since several arboviral infections result in acute self limiting fever they have remained unsuspected for several decades. However, it is well known that during the 1980's intensive malaria control initiatives which included massive distribution of bed nets, community education and indoor and outdoor spraying campaigns were implemented. It is possible that these measures may have influenced the epidemiology of arboviruses. However, the impact of these interventions in controlling the spread of arboviruses is not known.In conclusion, the old literature on arboviruses in Mozambique is relevant for assessing the gaps and current risk of occurrence of these pathogens at the region, particularly in a time in which they are spreading worldwide.

Arabidopsis thaliana plants expressing Rift Valley fever virus antigens: Mice exhibit systemic immune responses as the result of oral administration of the transgenic plants.

The zoonotic Rift Valley fever virus affects livestock and humans in Africa and on the Arabian Peninsula. The economic impact of this pathogen due to livestock losses, as well as its relevance to public health, underscores the importance of developing effective and easily distributed vaccines. Vaccines that can be delivered orally are of particular interest. Here, we report the expression in transformed plants (Arabidopsis thaliana) of Rift Valley fever virus antigens. The antigens used in this study were the N protein and a deletion mutant of the Gn glycoprotein. Transformed lines were analysed for specific mRNA and protein content by RT-PCR and Western blotting, respectively. Furthermore, the plant-expressed antigens were evaluated for their immunogenicity in mice fed the transgenic plants. After oral intake of fresh transgenic plant material, a proportion of the mice elicited specific IgG antibody responses, as compared to the control animals that were fed wild-type plants and of which none sero-converted. Thus, we show that transgenic plants can be readily used to express and produce Rift Valley Fever virus proteins, and that the plants are immunogenic when given orally to mice. These are promising findings and provide a basis for further studies on edible plant vaccines against the Rift Valley fever virus.

Multiplex nucleic acid suspension bead arrays for detection and subtyping of filoviruses.

Here we describe multiplex suspension bead array systems that allow fast and reliable detection of reverse transcriptase (RT) PCR amplified filovirus genomes and also enable subtyping of Ebola virus species and Marburg virus strains. These systems have an analytical sensitivity equivalent to that of RT-PCR.

One-step real-time RT-PCR assays for serotyping dengue virus in clinical samples.

BACKGROUND: Dengue is one of the leading causes of morbidity in tropical and subtropical regions and infection with any of the four dengue virus serotypes (DENV1-4) result in a wide range of clinical manifestations. Given the geographic expansion of DENV1-4, assays for serotyping are needed to be able to perform surveillance and epidemiological studies. In this study, we describe the design and validation of one-step real-time serotype-specific DENV RT-PCR assays. METHODS: The DENV1, DENV2, DENV3, and DENV4 RT-PCR assays were designed using all available whole genome DENV sequences in the NCBI nucleotide collection. Because of the high mutation rates of RNA viruses, the assays were performed in singleplex format to enable quick modifications to the primer and probe sequences when new genetic variants emerge. The analytical performance of the RT-PCR assays were evaluated using in vitro transcribed RNA and their specificity was determined by testing 24 DENV isolates, external DENV control panels and RNA preparation of non-DENV flaviviruses and non-dengue clinical samples. Additionally, the clinical performance of the serotype-specific DENV RT-PCR were compared to that of the CDC DENV-1-4 RT-PCR using 85 clinical samples collected from patients presenting with acute dengue. RESULTS: The RT-PCR assays were found to be specific for their respective serotype and did not cross-react with other flaviviruses or human mRNA. All assays had a linear dynamic range of 10(2) to 10(6) copies/reaction with detection limits between 12 and 44 copies/reaction. When testing sera from 85 confirmed acute dengue cases, the serotype-specific DENV RT-PCR assays had 100 % positive agreement with the FDA-approved CDC DENV-1-4 RT-PCR assay performed in a singleplex format. Additionally 15 samples that tested negative in the CDC DENV-1-4- RT-PCR assay were found positive using the serotype-specific DENV RT-PCR assays. CONCLUSIONS: Our results suggest that these RT-PCR assays are useful alternatives to existing methods for serotyping DENV in clinical sera.

Interleaflet sliding in lipidic bilayers under shear flow: comparison of the gel and fluid phases using reversed non-equilibrium molecular dynamics simulations.

The friction between two rubbing surfaces lubricated by water can be diminished if they are coated with phospholipidic bilayers or brushes of polyelectrolytes. In the case of a coating by lipid membranes, the friction is lower when the lipids are in the gel phase rather than in the liquid phase. We investigated the response of fluid or gel bilayers to a mechanical load or under shear using non-equilibrium molecular dynamics simulations (NEMD) to understand whether this difference could come from intermonolayer sliding. The system is composed of a single fully hydrated bilayer of coarse grained phospholipids under a parallel shear with vorticity parallel to the bilayer. In both the liquid and the gel phases, an intermonolayer slip was measured in the velocity profile. In the liquid phase this slip is proportional to the shear stress. In the tilted gel phase of our model the stress is not systematically linear and relaxes differently when the shear is in the direction of the tilt or perpendicular to it. The impact of surface tension (or load) on the friction is different for the liquid and gel phases, but grossly the slip remains of the same order of magnitude.

Toward a continuum description of lubrication in highly pressurized nanometer-wide constrictions: The importance of accurate slip laws.

The Reynolds lubrication equation (RLE) is widely used to design sliding contacts in mechanical machinery. While providing an excellent description of hydrodynamic lubrication, friction in boundary lubrication regions is usually considered by empirical laws, because continuum theories are expected to fail for lubricant film heights h0 ≪ 10 nm, especially in highly loaded tribosystems with normal pressures pn ≫ 0.1 GPa. Here, the performance of RLEs is validated by molecular dynamics simulations of pressurized (with pn = 0.2 to 1 GPa) hexadecane in a gold converging-diverging channel with minimum gap heights h0 = 1.4 to 9.7 nm. For pn ≤ 0.4 GPa and h0 ≥ 5 nm, agreement with the RLE requires accurate constitutive laws for pressure-dependent density and viscosity. An additional nonlinear wall slip law relating wall slip velocities to local shear stresses extends the RLE's validity to even the most severe loading condition pn = 1 GPa and h0 = 1.4 nm. Our results demonstrate an innovative route for continuum modeling of highly loaded tribological contacts under boundary lubrication.

Ultralow liquid/solid friction in carbon nanotubes: comprehensive theory for alcohols, alkanes, OMCTS, and water.

In this work, we perform a theoretical study of liquid flow in graphitic nanopores of different sizes and geometries. Molecular dynamics flow simulations of different liquids (water, decane, ethanol, and OMCTS) in carbon nanotubes (CNT) are shown to exhibit flow velocities 1-3 orders of magnitude higher than those predicted from the continuum hydrodynamics framework and the no-slip boundary condition. These results support previous experimental findings obtained by several groups that reported exceptionally high liquid flow rates in CNT membranes. The liquid/graphite friction coefficient is identified as the crucial parameter for this fast mass transport in CNT. The friction coefficient is found to be very sensitive to wall curvature: friction is independent of confinement for liquids between flat graphene walls with zero curvature, whereas it decreases with increasing positive curvature (liquid inside CNT), and it increases with increasing negative curvature (liquid outside CNT). Furthermore, we present a theoretical approximate expression for the friction coefficient, which predicts qualitatively and semiquantitatively its curvature dependent behavior. The proposed theoretical description, which works well for different kinds of liquids (alcohols, alkanes, and water), sheds light on the physical mechanisms at the origin of the ultra low liquid/solid friction in CNT. In fact, it is due to their perfectly ordered molecular structure and their atomically smooth surface that carbon nanotubes are quasiperfect liquid conductors compared to other membrane pores like nanochannels in amorphous silica.

Relating Dry Friction to Interdigitation of Surface Passivation Species: A Molecular Dynamics Study on Amorphous Carbon.

Friction in boundary lubrication is strongly influenced by the atomic structure of the sliding surfaces. In this work, friction between dry amorphous carbon (a-C) surfaces with chemisorbed fragments of lubricant molecules is investigated employing molecular dynamic simulations. The influence of length, grafting density and polarity of the fragments on the shear stress is studied for linear alkanes and alcohols. We find that the shear stress of chain-passivated a-C surfaces is independent of the a-C density. Among all considered chain-passivated systems, those with a high density of chains of equal length exhibit the lowest shear stress. However, shear stress in chain-passivated a-C is consistently higher than in a-C surfaces with atomic passivation. Finally, surface passivation species with OH head groups generally lead to higher friction than their non-polar analogs. Beyond these qualitative trends, the shear stress behavior for all atomic- and chain-passivated, non-polar systems can be explained semi-quantitatively by steric interactions between the two surfaces that cause resistance to the sliding motion. For polar passivation species electrostatic interactions play an additional role. A corresponding descriptor that properly captures the interlocking of the two surfaces along the sliding direction is developed based on the maximum overlap between atoms of the two contacting surfaces.

Systematic screening of BK virus by real-time PCR prevents BK virus associated nephropathy in renal transplant recipients.

BK virus associated nephropathy occurs in approximately 5% of renal transplant recipients. Quantitation of BKV DNA in serum/plasma early in the course of disease has been suggested to be an important diagnostic tool for polymavirus-associated nephropathy (PVAN). The aim of this study was to develop a BKV real-time PCR (qPCR), which could be included in a diagnostic qPCR platform. Additionally, the significance of the assay as a surrogate marker for PVAN was investigated. Quantitation of BKV DNA by qPCR was carried out on 234 serum samples from a retrospective study including 31 renal transplant recipients monitored for at least 6 months post-transplantation. BKV viremia was detected in 9 out of 31 patients. Four patients had a viral load of >10,000 copies/ml at least on one occasion. In two of these patients, PVAN was diagnosed clinically during the study period. In retrospect, these patients were shown to be BKV positive before the clinical diagnosis of PVAN was made. Another two patients had a permanent graft dysfunction, but were never clinically diagnosed with PVAN. None of the remaining five patients with BKV DNA (<10,000 copies/ml) had renal impairment. Based on these results, an algorithm was introduced at the study center in 2006 and to date, August 2011, no cases of PVAN with loss of graft have been observed. The concept of including different PCR protocols in a common qPCR platform allows laboratories with small sample numbers to perform regularly a variety of assays at a reasonable cost.

Primary infection with the Epstein-Barr virus and risk of multiple sclerosis.

To determine whether multiple sclerosis (MS) risk increases following primary infection with the Epstein-Barr virus (EBV), we conducted a nested case-control study including 305 individuals who developed MS and 610 matched controls selected among the >8 million active-duty military personnel whose serum has been stored in the Department of Defense Serum Repository. Time of EBV infection was determined by measuring antibody titers in serial serum samples collected before MS onset among cases, and on matched dates among controls. Ten (3.3%) cases and 32 (5.2%) controls were initially EBV negative. All of the 10 EBV-negative cases became EBV positive before MS onset; in contrast, only 35.7% (n = 10) of the 28 controls with follow-up samples seroconverted (exact p value = 0.0008). We conclude that MS risk is extremely low among individuals not infected with EBV, but it increases sharply in the same individuals following EBV infection.

Molecular origin of fast water transport in carbon nanotube membranes: superlubricity versus curvature dependent friction.

In this paper, we study the interfacial friction of water at graphitic interfaces with various topologies, water between planar graphene sheets, inside and outside carbon nanotubes, with the goal to disentangle confinement and curvature effects on friction. We show that the friction coefficient exhibits a strong curvature dependence; while friction is independent of confinement for the graphene slab, it decreases with carbon nanotube radius for water inside, but increases for water outside. As a paradigm the friction coefficient is found to vanish below a threshold diameter for armchair nanotubes. Using a statistical description of the interfacial friction, we highlight here a structural origin of this curvature dependence, mainly associated with a curvature-induced incommensurability between the water and carbon structures. These results support the recent experiments reporting fast transport of water in nanometric carbon nanotube membranes.

Anchored pan dengue RT-PCR and fast sanger sequencing for detection of dengue RNA in human serum.

A large number of human infections are caused by different dengue virus strains, mainly in the tropical and subtropical parts of the world, but also outside the endemic regions. RT-PCR methods are used widely for detection of dengue virus RNA in acute-phase serum samples; however, new sequence variation can inhibit these methods. An assay was developed integrating an anchored Pan Dengue RT-PCR with a new Fast Sanger sequencing protocol. For broad detection and identification of dengue virus RNA, including new strains of all serotypes, the conserved 3' genome end was targeted for highly specific cDNA synthesis. A combination of degenerated primers was used for second strand synthesis, followed by tag primed amplification. The mixture of generated amplicons was identified directly by the Fast Sanger sequencing from the anchored 3' genome end. Evaluating the assay on human serum RNA spiked with viral RNA representing the four dengue serotypes demonstrated a detection limit of 44-124 copies viral RNA per reaction for a two-step format of the anchored Pan Dengue RT-PCR and 100-500 copies for a one-step protocol, respectively. The different serotypes were clearly identified from the generated sequences. Further, the 5-hr procedure was evaluated and compared to standard real-time RT-PCR protocols on acute-phase serum samples from patients with confirmed dengue infections. This assay demonstrates a strategy for virus detection, which combines nucleic acid amplification adapted for dengue virus RNA with direct and rapid sequencing. It provides a tolerance for new sequence variation and the strategy should be applicable for other RNA viruses.

Population differences in immune marker profiles associated with human T-lymphotropic virus type I infection in Japan and Jamaica.

The natural history of human T-lymphotropic virus type I (HTLV-I) has been shown to differ markedly by geographic area. The differences include contrasting patterns of risk of adult T-cell lymphoma (ATL) and HTLV-I-associated myelopathy/tropical spastic paraparesis (HAM/TSP), which may be due in part to differences in host immune response to infection. To characterize variations in host immunity across populations, we compared serologic immune marker patterns in HTLV-I-endemic populations in Japan and Jamaica. We matched 204 participants with archived blood from the Miyazaki Cohort Study (Japan) and the Food Handlers Study (Jamaica)-i.e., 51 HTLV-I-positive ("carriers") and 51 HTLV-I-negative individuals ("noncarriers") from each population-by age, sex and blood collection year. We compared plasma concentrations of markers of T-cell-mediated (antigen-specific) and nonspecific immunity using regression models and correlation coefficients. Compared to Jamaican HTLV-I noncarriers, Japanese noncarriers had higher covariate-adjusted mean levels of T-cell activation markers, including antibody to Epstein-Barr virus nuclear antigen-1 (reciprocal titer 27 vs. 71, respectively, p=0.005), soluble interleukin-2 receptor-alpha (477 vs. 623 pg/mL, p=0.0008) and soluble CD30 (34 vs. 46 U/mL, p=0.0001) and lower levels of C-reactive protein (1.1 vs. 0.43 microg/mL, p=0.0004). HTLV-I infection was associated with activated T-cell immunity in Jamaicans but with diminished T-cell immunity in Japanese persons. The observed population differences in background and HTLV-I-related host immunity correspond closely to the divergent natural histories of infection observed among HTLV-I carriers in Japan and Jamaica and corroborate a role for host immune status in the contrasting patterns of ATL and HAM/TSP risk.

A molecular link between malaria and Epstein-Barr virus reactivation.

Although malaria and Epstein-Barr (EBV) infection are recognized cofactors in the genesis of endemic Burkitt lymphoma (BL), their relative contribution is not understood. BL, the most common paediatric cancer in equatorial Africa, is a high-grade B cell lymphoma characterized by c-myc translocation. EBV is a ubiquitous B lymphotropic virus that persists in a latent state after primary infection, and in Africa, most children have sero-converted by 3 y of age. Malaria infection profoundly affects the B cell compartment, inducing polyclonal activation and hyper-gammaglobulinemia. We recently identified the cystein-rich inter-domain region 1alpha (CIDR1alpha) of the Plasmodium falciparum membrane protein 1 as a polyclonal B cell activator that preferentially activates the memory compartment, where EBV is known to persist. Here, we have addressed the mechanisms of interaction between CIDR1alpha and EBV in the context of B cells. We show that CIDR1alpha binds to the EBV-positive B cell line Akata and increases the number of cells switching to the viral lytic cycle as measured by green fluorescent protein (GFP) expression driven by a lytic promoter. The virus production in CIDR1alpha-exposed cultures was directly proportional to the number of GFP-positive Akata cells (lytic EBV) and to the increased expression of the EBV lytic promoter BZLF1. Furthermore, CIDR1alpha stimulated the production of EBV in peripheral blood mononuclear cells derived from healthy donors and children with BL. Our results suggest that P. falciparum antigens such as CIDR1alpha can directly induce EBV reactivation during malaria infection that may increase the risk of BL development for children living in malaria-endemic areas. To our knowledge, this is the first report to show that a microbial protein can drive a latently infected B cell into EBV replication.

Monitoring of herpes simplex virus DNA types 1 and 2 viral load in cerebrospinal fluid by real-time PCR in patients with herpes simplex encephalitis.

A quantitative polymerase chain reaction (PCR) assay was evaluated retrospectively on 92 cerebrospinal fluid (CSF) samples from 29 patients with herpes simplex virus (HSV) encephalitis with the aim to study if the concentration of HSV genomes can be used as a prognostic marker and for monitoring of antiviral therapy. The results were compared to those obtained previously by nested PCR, and the numbers of HSV genomes/ml were evaluated in correlation to patient outcome and treatment. The aims were to compare the sensitivity of a conventional nested PCR to a quantitative PCR, to investigate the range of HSV genome concentration in initial samples and to evaluate possible relationships between the HSV DNA concentrations in CSF, neopterin levels, and outcome of disease. The 29 initial samples contained between 2 x 10(2) and 42 x 10(6) HSV genomes/ml. There was no apparent correlation between the amount of HSV DNA in the initial samples and income status, initial neopterin levels, or prognosis. The number of HSV genomes/ml declined after treatment in all patients, but HSV DNA was still detectable after day 20 in 3 out of 16 patients. A long duration of genome detectability was found to correlate with poor outcome. There was no difference in sensitivity between the nested PCR and the quantitative PCR. While the quantitative PCR is more rational than a nested PCR, the quantitation of HSV genomes does not seem very useful as a prognostic marker in HSV encephalitis.

Puumala hantavirus excretion kinetics in bank voles (Myodes glareolus).

Puumala hantavirus is present in bank voles (Myodes glareolus) and is believed to be spread mainly by contaminated excretions. In this study, we subcutaneously inoculated 10 bank voles with Puumala virus and sampled excretions until day 133 postinfection. Levels of shed viral RNA peaked within 11-28, 14-21, and 11-28 days postinfection for saliva, urine, and feces, respectively. The latest detection of viral RNA was 84, 44, and 44 days postinfection in saliva, urine, and feces, respectively. In contrast, blood of 5 of 6 animals contained viral RNA at day 133 postinfection, suggesting that bank voles secrete virus only during a limited time of the infection. Intranasal inoculations with bank vole saliva, urine, or feces were all infectious for virus-negative bank voles, indicating that these 3 transmission routes may occur in nature and that rodent saliva might play a role in transmission to humans.

Viral metagenomics reveals the presence of highly divergent quaranjavirus in Rhipicephalus ticks from Mozambique.

Background: Ticks are primary vectors for many well-known disease-causing agents that affect human and animal populations globally such as tick-borne encephalitis, Crimean-Congo hemorrhagic fever and African swine fever. In this study, viral metagenomics was used to identify what viruses are present in Rhipicephalus spp. ticks collected in the Zambezi Valley of Mozambique. Methods: The RNA was amplified with sequence-independent single primer amplification (SISPA) and high-throughput sequencing was performed on the Ion Torrent platform. The generated sequences were subjected to quality check and classfied by BLAST. CodonCode aligner and SeqMan were used to assemble the sequences. Results: The majority of viral sequences showed closest sequence identity to the Orthomyxoviridae family, although viruses similar to the Parvoviridae and Coronaviridae were also identified. Nearly complete sequences of five orthomyxoviral segments (HA, NP, PB1, PB2, and PA) were obtained and these showed an amino acid identity of 32-52% to known quaranjaviruses. The sequences were most closely related to the Wellfleet Bay virus, detected and isolated from common eider during a mortality event in the USA. Conclusions: In summary, this study has identified a highly divergent virus with in the Orthomyxoviridae family associated with Rhipicephalus ticks from Mozambique. Further genetic and biological studies are needed in order to investigate potential pathogenesis of the identified orthomyxovirus.