bluuebunny/crossref_metadata_2025 huggingface dataset:
A Zero-Spin Design Methodology for Transmission Components Generatrix in Traction Drive Continuously Variable Transmissions
Authors: Li Qingtao , Liao Min , Wang Shuang
Published: December 2017

With the advantages of high torque and low noise, traction drive continuously variable transmissions (TDCVTs) have a promising application in future vehicles. However, their efficiency is limited by spin losses caused by the different speed distributions between the contact areas of the traction. To overcome this shortcoming, this paper proposes a novel zero-spin design methodology applicable to any type of TDCVTs. The methodology analyzes the features of TDCVTs in terms of the variation of contact position and the shifting motion of traction components. It also establishes a mathematical model resulting in differential equations, whose general solution is the substitute for the equation of traction components generatrix. After applications of the methodology to two original TDCVTs, two zero-spin TDCVTs are proposed. A computational method of spin ratios, which are in direct proportion to spin losses, of four TDCVTs is introduced. The results of comparisons demonstrate that the proposed methodology can dramatically reduce the spin losses.
Near Time-Optimal Real-Time Path Following Under Error Tolerance and System Constraints
Authors: Chang Yen-Chi , Chen Cheng-Wei , Tsao Tsu-Chin
Published: December 2017

An online fast path following control algorithm subject to contouring error tolerance and other prototypical constraints, analogous to a racing car within track boundaries, is presented. A receding horizon quadratic programming (QP) for real-time implementation on electromechanical systems is proposed. A key feature of the algorithm is that the challenging constrained minimal-time optimization is approximated by minimizing the distance between an unattainable target and actual location when moving along the contour, mimicking pursuing rabbit lures in greyhound racing. Modeling errors and other uncertainties in implementation are compensated for by observer state feedback, which provides real-time updates of initial states for every receding horizon optimization. Applying the proposed online method, the requirement of an accurate model from conventional offline trajectory planning methods is relaxed. The proposed method is demonstrated by experimental results from a 1 kHz sampling rate implementation on a multi-axis nanolithographic position system.
Loss of Optimal Performance of the Finite-Horizon Continuous-Time Linear-Quadratic Controller Driven by a Reduced-Order Observer
Authors: Radisavljevic-Gajic Verica , Milanovic Milos
Published: December 2017

In this paper, we derive an expression for the loss of optimal performance (compared to the corresponding linear-quadratic optimal performance with the instantaneous full-state feedback) when the continuous-time finite-horizon linear-quadratic optimal controller uses the estimates of the state variables obtained via a reduced-order observer. It was shown that the loss of optimal performance value can be found by solving the differential Lyapunov equation whose dimensions are equal to dimensions of the reduced-order observer. A proton exchange membrane fuel cell example is included to demonstrate the loss of optimal performance as a function of the final time. It can be seen from the simulation results that the loss of optimal performance value can be very large. The loss of optimal performance value can be drastically reduced by using the proposed least-square formulas for the choice of the reduced-order observer initial conditions.
Two Degrees-of-Freedom Fractional-Order Proportional–Integral–Derivative-Based Temperature Control of Fermentation Process
Authors: Pachauri Nikhil , Singh Vijander , Rani Asha
Published: December 2017

Temperature is one of the essential parameter in a fermentation process, which affects the thermal movement of cells. The temperature range for such processes is very tight and must be maintained precisely for efficient operation. Therefore, in this work combination of fractional calculus and two degrees-of-freedom proportional–integral–derivative (2DOF-PID) controller is proposed for desired temperature control of bioreactor. The 2DOF-PID controller incorporates an extra control loop, whereas fractional operator offers additional tractability for alteration in system dynamics. In order to achieve efficient execution of the control strategies, design parameters are optimized with the help of nondominated sorted genetic algorithm-II (NSGA-II) and Cuckoo search algorithm (CSA). NSGA-II-tuned controllers perform better than the CSA-tuned controllers. Further, the results show that the proposed controller regulates the temperature of bioreactor in a more robust and efficient manner in comparison to other designed controllers.
Laser Surface Engineering of Hierarchy Hydroxyapatite Aerogel for Bone Tissue Engineering
Authors: Parandoush Pedram , Fan Hanxiong , Song Xiaolei , Lin Dong
Published: December 2017

Bioceramics with porous microstructure has attracted intense attention in tissue engineering due to tissue growth facilitation in the human body. In the present work, a novel manufacturing process for producing hydroxyapatite (HA) aerogels with a high density shell inspired by human bone microstructure is proposed for bone tissue engineering applications. This method combines laser processing and traditional freeze casting, in which HA aerogel is prepared by freeze casting and aqueous suspension prior to laser processing of the aerogel surface with a focused CO2 laser beam that forms a dense layer on top of the porous microstructure. Using the proposed method, HA aerogel with dense shell was successfully prepared with a microstructure similar to human bone. The effect of laser process parameters on the surface, cross-sectional morphology and microstructure was investigated in order to obtain optimum parameters and has a better understanding of the process. Low laser energy resulted in a fragile thin surface with defects and cracks due to the thermal stress induced by the laser processing. However, increasing the laser power generated a thicker dense layer on the surface, free of defects. The range of 40–45 W laser power, 5 mm/s scanning speed, spot size of 1 mm, and 50% overlap in laser scanning the surface yielded the best surface morphology and microstructure in our experiments.
Paperless Arrests as Preventive Detention: Motion and Documentation in the Governance of Indigenous Peoples of Australia
Authors: Grealy Liam
Published: December 2017

The ‘paperless arrest’ scheme is a detention regime in which motion and documentation are central to crime control and community protection. This article interrogates paperlessness as a political fantasy for policing alongside the routine documentary practices of police administration, including their effects on the movement of Aboriginal and Torres Strait Islander people. Operative since 2014 in Australia’s Northern Territory (NT), the paperless arrest scheme provides police with the power to take an individual into custody for up to four hours if they believe, on reasonable grounds, that the individual has committed, or was about to commit, an infringement notice offence. This article frames paperless arrests as an instance of preventive detention continuous with the long-term regulation of alcohol consumption by Aboriginal people, in relation to racialised norms of public propriety in urban space. It considers preventive detention beyond issues of legality and efficacy, examining local and material relations that organise the everyday governance of preventive detention in Northern Australia.
Space, Race, Bodies – A Conference Theme, A Timely Reminder
Authors: Jackson Moana
Published: December 2017

Moana's commentary on the Space, Race, Bodis II conference
L’Ordre et la Morale: Looking Beyond the Transnational in a Non-indigenous Film About Recent Pacific History
Authors: Speedy Karin Elizabeth
Published: December 2017

Most films about the Pacific may be described as transnational in terms of production (and often content), but is it ever possible, within a Postcolonial or Indigenous critique, to move beyond conversations about appropriation? And is the transnational aspect of the film the most useful way to categorise it? Specifically engaging with the Mathieu Kassovitz film L’Ordre et la morale, a retelling of the 1988 French military assault on Kanak hostage-takers in Ouvéa, New Caledonia, this article explores whether we can reconcile the twin dangers of Pacific narratives going untold (and the consequent erasure felt by Indigenous people) versus the peril of Pasifika people seeing only shallow, erroneous, or negative stereotypes of themselves on screen. What role, if any, can non-Indigenous filmmakers play in the cinematic reproduction of Indigenous Pacific histories?
Leaving Politics Behind? Diasporic Nationalism in London
Authors: Humpage Louise
Published: December 2017

Up to a million New Zealanders live overseas at any one time, many residing in London. Exploratory research with members of New Zealand-oriented civil society organisations established in London highlights a strong perception that the expatriate experience provides a certain distance from New Zealand politics – particularly ‘bicultural’ politics – that encourages boundary-crossing relationships and a stronger sense of belonging amongst Māori than experienced at home. This is an important finding but this article questions whether such politics are really absent, since interview data reveals that London-based organisations and their members undertake significant ‘political’ work in connecting expatriate citizens to ‘home’ and in protecting New Zealand’s reputation. These activities reinforce forms of nostalgia that prioritise European/Pākehā norms and, ultimately, fail to acknowledge ongoing tensions in New Zealand’s national story.
Reshaping the Landscape of Care: Health Apps and the Ethics of Self-responsibility and Care for the Other
Authors: Trnka Susanna , Merino Ortiz Andrea
Published: December 2017

This article considers the ethical implications of health apps, focusing on how digital technologies create new temporalities of care for the self and for others. Drawing on our own experiences of engaging in digital care, we examine how apps that focus on mood/emotion tracking, mental health, meditation, and other forms of stress-relief reconfigure inter-relationality. Recasting how information is shared as well as the temporal possibilities of social exchanges, such health apps enable "friends" we know or are coming to know, as well as those we do not want to know, to enter into some of the most intimate aspects of our lives, as they unfold in the open-ended flow of time. In doing so, health apps, we suggest, demand a rethinking of the ethics of how we constitute and care for both the self and a variety of (known and unknown) others.
Clinical trial design: The nobility of randomization
Authors: Michael Nelson L.
Published: December 2017

A clinical trial evaluating HIV vaccine therapy teaches us much about optimal design (Sneller
et al
., this issue).
Breaking free from the NETs
Authors: Levi Benjamin
Published: December 2017

Neutrophil extracellular traps exacerbate ischemia reperfusion injury associated with neonatal midgut volvulus and serve as a therapeutic target.
Taking control of a volatile situation
Authors: Philips Jennifer A.
Published: December 2017

A 3D microscale model of the human bronchiole reveals volatile-mediated communication between
Aspergillus
,
Pseudomonas
, and host.
Diagnostic Assay Development for Poliovirus Eradication
Authors: Gerloff Nancy , Sun Hong , Mandelbaum Mark , Maher Chelsea , Nix W. Allan , Zaidi Sohail , Shaukat Shahzad , Seakamela Lerato , Nalavade Uma P. , Sharma Deepa K. , Oberste M. Steven , Vega Everardo
Published: December 2017

With poliovirus eradication nearing, few pockets of active wild poliovirus (WPV) transmission remain in the world. Intratypic differentiation (ITD) plays a crucial part in laboratory surveillance as the molecular detection method that can identify and distinguish wild and vaccine-like polioviruses isolated from acute flaccid paralysis cases or environmental sources. The need to detect new variants of WPV serotype 1 (WPV1) and the containment of all serotype 2 polioviruses (PV2) in 2015 required changes to the previous version of the method. The ITD version 5.0 is a set of six real-time reverse transcription-PCR (rRT-PCR) assays that serve as accurate diagnostic tools to easily detect and differentiate PV serotypes and genotypes. We describe the creation and properties of quantitation standards, including 16 control RNA transcripts and nine plaque-isolated viruses. All ITD rRT-PCR assays were validated using these standards, and the limits of detection were determined for each assay. We designed and pilot tested two new assays targeting recently circulating WPV1 genotypes and all PV2 viruses. The WPV1 assay had 99.1% specificity and 100% sensitivity, and the PV2 assay had 97.7% specificity and 92% sensitivity. Before proceeding to the next step in the global poliovirus eradication program, we needed to gain a better understanding of the performance of the ITD 5.0 suite of molecular assays and their limits of detection and specificities. The findings and conclusions in this evaluation serve as building blocks for future development work.
Characterization of Influenza Virus Pseudotyped with Ebolavirus Glycoprotein
Authors: Xiao Julie Huiyuan , Rijal Pramila , Schimanski Lisa , Tharkeshwar Arun Kumar , Wright Edward , Annaert Wim , Townsend Alain
Published: December 2017

We have produced a new Ebola virus pseudotype, E-S-FLU, that can be handled in biosafety level 1/2 containment for laboratory analysis. The E-S-FLU virus is a single-cycle influenza virus coated with Ebolavirus glycoprotein, and it encodes enhanced green fluorescence protein as a reporter that replaces the influenza virus hemagglutinin. MDCK-SIAT1 cells were transduced to express Ebolavirus glycoprotein as a stable transmembrane protein for E-S-FLU virus production. Infection of cells with the E-S-FLU virus was dependent on the Niemann-Pick C1 protein, which is the well-characterized receptor for Ebola virus entry at the late endosome/lysosome membrane. The E-S-FLU virus was neutralized specifically by an anti-Ebolavirus glycoprotein antibody and a variety of small drug molecules that are known to inhibit the entry of wild-type Ebola virus. To demonstrate the application of this new Ebola virus pseudotype, we show that a single laboratory batch was sufficient to screen a library (LOPAC
1280
; Sigma) of 1,280 pharmacologically active compounds for inhibition of virus entry. A total of 215 compounds inhibited E-S-FLU virus infection, while only 22 inhibited the control H5-S-FLU virus coated in H5 hemagglutinin. These inhibitory compounds have very dispersed targets and mechanisms of action, e.g., calcium channel blockers, estrogen receptor antagonists, antihistamines, serotonin uptake inhibitors, etc., and this correlates with inhibitor screening results obtained with other pseudotypes or wild-type Ebola virus in the literature. The E-S-FLU virus is a new tool for Ebola virus cell entry studies and is easily applied to high-throughput screening assays for small-molecule inhibitors or antibodies.

IMPORTANCE
Ebola virus is in the
Filoviridae
family and is a biosafety level 4 pathogen. There are no FDA-approved therapeutics for Ebola virus. These characteristics warrant the development of surrogates for Ebola virus that can be handled in more convenient laboratory containment to study the biology of the virus and screen for inhibitors. Here we characterized a new surrogate, named E-S-FLU virus, that is based on a disabled influenza virus core coated with the Ebola virus surface protein but does not contain any genetic information from the Ebola virus itself. We show that E-S-FLU virus uses the same cell entry pathway as wild-type Ebola virus. As an example of the ease of use of E-S-FLU virus in biosafety level 1/2 containment, we showed that a single production batch could provide enough surrogate virus to screen a standard small-molecule library of 1,280 candidates for inhibitors of viral entry.
Autographa californica Multiple Nucleopolyhedrovirus
ac75
Is Required for the Nuclear Egress of Nucleocapsids and Intranuclear Microvesicle Formation
Authors: Shi Anqi , Hu Zhaoyang , Zuo Yachao , Wang Yan , Wu Wenbi , Yuan Meijin , Yang Kai
Published: December 2017

Autographa californica multiple nucleopolyhedrovirus (AcMNPV)
orf75
(
ac75
) is a highly conserved gene of unknown function. In this study, we constructed an
ac75
knockout AcMNPV bacmid and investigated the role of
ac75
in the baculovirus life cycle. The expression and distribution of the Ac75 protein were characterized, and its interaction with another viral protein was analyzed to further understand its function. Our data indicated that
ac75
was required for the nuclear egress of nucleocapsids, intranuclear microvesicle formation, and subsequent budded virion (BV) formation, as well as occlusion-derived virion (ODV) envelopment and embedding of ODVs into polyhedra. Western blot analyses showed that two forms, of 18 and 15 kDa, of FLAG-tagged Ac75 protein were detected. Ac75 was associated with both nucleocapsid and envelope fractions of BVs but with only the nucleocapsid fraction of ODVs; the 18-kDa form was associated with only BVs, whereas the 15-kDa form was associated with both types of virion. Ac75 was localized predominantly in the intranuclear ring zone during infection and exhibited a nuclear rim distribution during the early phase of infection. A phase separation assay suggested that Ac75 was not an integral membrane protein. A coimmunoprecipitation assay revealed an interaction between Ac75 and the integral membrane protein Ac76, and bimolecular fluorescence complementation assays identified the sites of the interaction within the cytoplasm and at the nuclear membrane and ring zone in AcMNPV-infected cells. Our results have identified
ac75
as a second gene that is required for both the nuclear egress of nucleocapsids and the formation of intranuclear microvesicles.

IMPORTANCE
During the baculovirus life cycle, the morphogenesis of both budded virions (BVs) and occlusion-derived virions (ODVs) is proposed to involve a budding process at the nuclear membrane, which occurs while nucleocapsids egress from the nucleus or when intranuclear microvesicles are produced. However, the exact mechanism of virion morphogenesis remains unknown. In this study, we identified
ac75
as a second gene, in addition to
ac93
, that is essential for the nuclear egress of nucleocapsids, intranuclear microvesicle formation, and subsequent BV formation, as well as ODV envelopment and embedding of ODVs into polyhedra. Ac75 is not an integral membrane protein. However, it interacts with an integral membrane protein (Ac76) and is associated with the nuclear membrane. These data enhance our understanding of the commonalities between nuclear egress of nucleocapsids and intranuclear microvesicle formation and may help to reveal insights into the mechanism of baculovirus virion morphogenesis.
Structural Insight into a Human Neutralizing Antibody against Influenza Virus H7N9
Authors: Chen Cong , Liu Liguo , Xiao Yan , Cui Sheng , Wang Jianmin , Jin Qi
Published: December 2017

Since its first emergence in East China in early 2013, many cases of avian influenza A H7N9 have been reported. The disease has extended to 22 provinces in mainland China and some surrounding areas. Strategies to combat viral infection are urgently needed. We previously isolated a human monoclonal antibody, HNIgGA6, that neutralized the H7N9 virus both
in vitro
and
in vivo
. In this study, we determined the crystal structure of viral hemagglutinin (HA) globular head bound to the fragment antigen-binding region (Fab) of HNIgGA6. The crystal structure shows that the tip of the HNIgGA6 heavy-chain complementarity-determining region 3 (HCDR3) directly interposes into the receptor binding site (RBS) and mimics, in many respects, the interaction of the sialic acid receptor. Three residues at Y98, H183, and E190, which are critical to human cellular receptor binding, are also essential for HNIgGA6 recognition. Meanwhile, dual mutations at V186G and L226Q in RBS were able to disrupt viral HA1 binding with the antibody. Our study provides a better understanding of the mechanism for protective antibody recognition and a sound foundation for the design of therapeutic drugs and vaccines against H7N9 influenza.

IMPORTANCE
Neutralization by antibody is one of the most important mechanisms for a host to defend against viral infections. Human-originated antibody HNIgGA6 was generated in response to the natural infectious H7N9 virus and showed potential for use in suppression of H7N9 infection, with possible therapeutic implications. The crystal structure of the HNIgGA6/HA1 complex provided new insight into the protective immune response to H7N9 virus in humans, as well as possibilities for the development of effective H7N9 pandemic vaccines and antiviral molecules.
Control of Human T-Cell Leukemia Virus Type 1 (HTLV-1) Infection by Eliminating Envelope Protein-Positive Cells with Recombinant Vesicular Stomatitis Viruses Encoding HTLV-1 Primary Receptor
Authors: Tezuka Kenta , Okuma Kazu , Kuramitsu Madoka , Matsuoka Sahoko , Tanaka Reiko , Tanaka Yuetsu , Hamaguchi Isao
Published: December 2017

Human T-cell leukemia virus type 1 (HTLV-1) infection causes adult T-cell leukemia (ATL), which is frequently resistant to currently available therapies and has a very poor prognosis. To prevent the development of ATL among carriers, it is important to control HTLV-1-infected cells in infected individuals. Therefore, the establishment of novel therapies with drugs specifically targeting infected cells is urgently required. This study aimed to develop a potential therapy by generating recombinant vesicular stomatitis viruses (rVSVs) that lack an envelope glycoprotein G and instead encode an HTLV-1 receptor with human glucose transporter 1 (GLUT1), neuropilin 1 (NRP1), or heparan sulfate proteoglycans (HSPGs), including syndecan 1 (SDC1), designated VSVΔG-GL, VSVΔG-NP, or VSVΔG-SD, respectively. In an attempt to enhance the infectivity of rVSV against HTLV-1-infected cells, we also constructed rVSVs with a combination of two or three receptor genes, designated VSVΔG-GLN and VSVΔG-GLNS, respectively. The present study demonstrates VSVΔG-GL, VSVΔG-NP, VSVΔG-GLN, and VSVΔG-GLNS have tropism for HTLV-1 envelope (Env)-expressing cells. Notably, the inoculation of VSVΔG-GL or VSVΔG-NP significantly eliminated HTLV-1-infected cells under the culture conditions. Furthermore, in an HTLV-1-infected humanized mouse model, VSVΔG-NP was capable of efficiently preventing HTLV-1-induced leukocytosis in the periphery and eliminating HTLV-1-infected Env-expressing cells in the lymphoid tissues. In summary, an rVSV engineered to express HTLV-1 primary receptor, especially human NRP1, may represent a drug candidate that has potential for the development of unique virotherapy against HTLV-1de novoinfection.

IMPORTANCEAlthough several anti-ATL therapies are currently available, ATL is still frequently resistant to therapeutic approaches, and its prognosis remains poor. Control of HTLV-1de novoinfection or expansion of HTLV-1-infected cells in the carrier holds considerable promise for the prevention of ATL development. In this study, we developed rVSVs that specifically target and kill HTLV-1 Env-expressing cells (not ATL cells, which generally do not express Envin vivo) through replacement of the G gene with HTLV-1 receptor gene(s) in the VSV genome. Notably, an rVSV engineered to express human NRP1 controlled the number of HTLV-1-infected Env-expressing cellsin vitroandin vivo, suggesting the present approach may be a promising candidate for novel anti-HTLV-1 virotherapy in HTLV-1 carriers, including as a prophylactic treatment against the development of ATL.
Minor Capsid Protein L2 Polytope Induces Broad Protection against Oncogenic and Mucosal Human Papillomaviruses
Authors: Pouyanfard Somayeh , Spagnoli Gloria , Bulli Lorenzo , Balz Kathrin , Yang Fan , Odenwald Caroline , Seitz Hanna , Mariz Filipe C. , Bolchi Angelo , Ottonello Simone , Müller Martin
Published: December 2017

The amino terminus of the human papillomavirus (HPV) minor capsid protein L2 contains a major cross-neutralization epitope which provides the basis for the development of a broadly protecting HPV vaccine. A wide range of protection against different HPV types would eliminate one of the major drawbacks of the commercial, L1-based prophylactic vaccines. Previously, we have reported that insertion of the L2 epitope into a scaffold composed of bacterial thioredoxin protein generates a potent antigen inducing comprehensive protection against different animal and human papillomaviruses. We also reported, however, that although protection is broad, some oncogenic HPV types escape the neutralizing antibody response, if L2 epitopes from single HPV types are used as immunogen. We were able to compensate for this by applying a mix of thioredoxin proteins carrying L2 epitopes from HPV16, -31, and -51. As the development of a cost-efficient HPV prophylactic vaccines is one of our objectives, this approach is not feasible as it requires the development of multiple good manufacturing production processes in combination with a complex vaccine formulation. Here, we report the development of a thermostable thioredoxin-based single-peptide vaccine carrying an L2 polytope of up to 11 different HPV types. The L2 polytope antigens have excellent abilities in respect to broadness of protection and robustness of induced immune responses. To further increase immunogenicity, we fused the thioredoxin L2 polytope antigen with a heptamerization domain. In the final vaccine design, we achieve protective responses against all 14 oncogenic HPV types that we have analyzed plus the low-risk HPVs 6 and 11 and a number of cutaneous HPVs.

IMPORTANCE
Infections by a large number of human papillomaviruses lead to malignant and nonmalignant disease. Current commercial vaccines based on virus-like particles (VLPs) effectively protect against some HPV types but fail to do so for most others. Further, only about a third of all countries have access to the VLP vaccines. The minor capsid protein L2 has been shown to contain so-called neutralization epitopes within its N terminus. We designed polytopes comprising the L2 epitope amino acids 20 to 38 of up to 11 different mucosal HPV types and inserted them into the scaffold of thioredoxin derived from a thermophile archaebacterium. The antigen induced neutralizing antibody responses in mice and guinea pigs against 26 mucosal and cutaneous HPV types. Further, addition of a heptamerization domain significantly increased the immunogenicity. The final vaccine design comprising a heptamerized L2 8-mer thioredoxin single-peptide antigen with excellent thermal stability might overcome some of the limitations of the current VLP vaccines.
Tetraspanin CD63 Bridges Autophagic and Endosomal Processes To Regulate Exosomal Secretion and Intracellular Signaling of Epstein-Barr Virus LMP1
Authors: Hurwitz Stephanie N. , Cheerathodi Mujeeb R. , Nkosi Dingani , York Sara B. , Meckes David G.
Published: December 2017

The tetraspanin protein CD63 has been recently described as a key factor in extracellular vesicle (EV) production and endosomal cargo sorting. In the context of Epstein-Barr virus (EBV) infection, CD63 is required for the efficient packaging of the major viral oncoprotein latent membrane protein 1 (LMP1) into exosomes and other EV populations and acts as a negative regulator of LMP1 intracellular signaling. Accumulating evidence has also pointed to intersections of the endosomal and autophagy pathways in maintaining cellular secretory processes and as sites for viral assembly and replication. Indeed, LMP1 can activate the mammalian target of rapamycin (mTOR) pathway to suppress host cell autophagy and facilitate cell growth and proliferation. Despite the growing recognition of cross talk between endosomes and autophagosomes and its relevance to viral infection, little is understood about the molecular mechanisms governing endosomal and autophagy convergence. Here, we demonstrate that CD63-dependent vesicle protein secretion directly opposes intracellular signaling activation downstream of LMP1, including mTOR-associated proteins. Conversely, disruption of normal autolysosomal processes increases LMP1 secretion and dampens signal transduction by the viral protein. Increases in mTOR activation following CD63 knockout are coincident with the development of serum-dependent autophagic vacuoles that are acidified in the presence of high LMP1 levels. Altogether, these findings suggest a key role of CD63 in regulating the interactions between endosomal and autophagy processes and limiting cellular signaling activity in both noninfected and virally infected cells.

IMPORTANCE
The close connection between extracellular vesicles and viruses is becoming rapidly and more widely appreciated. EBV, a human gamma herpesvirus that contributes to the progression of a multitude of lymphomas and carcinomas in immunocompromised or genetically susceptible populations, packages its major oncoprotein, LMP1, into vesicles for secretion. We have recently described a role of the host cell protein CD63 in regulating intracellular signaling of the viral oncoprotein by shuttling LMP1 into exosomes. Here, we provide strong evidence of the utility of CD63-dependent EVs in regulating global intracellular signaling, including mTOR activation by LMP1. We also demonstrate a key role of CD63 in coordinating endosomal and autophagic processes to regulate LMP1 levels within the cell. Overall, this study offers new insights into the complex intersection of cellular secretory and degradative mechanisms and the implications of these processes in viral replication.
Suppression of Zika Virus Infection and Replication in Endothelial Cells and Astrocytes by PKA Inhibitor PKI 14-22
Authors: Cheng Fan , Ramos da Silva Suzane , Huang I-Chueh , Jung Jae U. , Gao Shou-Jiang
Published: December 2017

The recent outbreak of Zika virus (ZIKV), a reemerging flavivirus, and its associated neurological disorders, such as Guillain-Barré (GB) syndrome and microcephaly, have generated an urgent need to develop effective ZIKV vaccines and therapeutic agents. Here, we used human endothelial cells and astrocytes, both of which represent key cell types for ZIKV infection, to identify potential inhibitors of ZIKV replication. Because several pathways, including the AMP-activated protein kinase (AMPK), protein kinase A (PKA), and mitogen-activated protein kinase (MAPK) signaling pathways, have been reported to play important roles in flavivirus replication, we tested inhibitors and agonists of these pathways for their effects on ZIKV replication. We identified the PKA inhibitor PKI 14-22 (PKI) to be a potent inhibitor of ZIKV replication. PKI effectively suppressed the replication of ZIKV from both the African and Asian/American lineages with a high efficiency and minimal cytotoxicity. While ZIKV infection does not induce PKA activation, endogenous PKA activity is essential for supporting ZIKV replication. Interestingly, in addition to PKA, PKI also inhibited another unknown target(s) to block ZIKV replication. PKI inhibited ZIKV replication at the postentry stage by preferentially affecting negative-sense RNA synthesis as well as viral protein translation. Together, these results have identified a potential inhibitor of ZIKV replication which could be further explored for future therapeutic application.

IMPORTANCE
There is an urgent need to develop effective vaccines and therapeutic agents against Zika virus (ZIKV) infection, a reemerging flavivirus associated with neurological disorders, including Guillain-Barré (GB) syndrome and microcephaly. By screening for inhibitors of several cellular pathways, we have identified the PKA inhibitor PKI 14-22 (PKI) to be a potent inhibitor of ZIKV replication. We show that PKI effectively suppresses the replication of all ZIKV strains tested with minimal cytotoxicity to human endothelial cells and astrocytes, two key cell types for ZIKV infection. Furthermore, we show that PKI inhibits ZIKV negative-sense RNA synthesis and viral protein translation. This study has identified a potent inhibitor of ZIKV infection which could be further explored for future therapeutic application.
Ecosystem Resilience and Limitations Revealed by Soil Bacterial Community Dynamics in a Bark Beetle-Impacted Forest
Authors: Mikkelson Kristin M. , Brouillard Brent M. , Bokman Chelsea M. , Sharp Jonathan O.
Published: December 2017

Forested ecosystems throughout the world are experiencing increases in the incidence and magnitude of insect-induced tree mortality with large ecologic ramifications. Interestingly, correlations between water quality and the extent of tree mortality in Colorado montane ecosystems suggest compensatory effects from adjacent live vegetation that mute responses in less severely impacted forests. To this end, we investigated whether the composition of the soil bacterial community and associated functionality beneath beetle-killed lodgepole pine was influenced by the extent of surrounding tree mortality. The most pronounced changes were observed in the potentially active bacterial community, where alpha diversity increased in concert with surrounding tree mortality until mortality exceeded a tipping point of ~30 to 40%, after which diversity stabilized and decreased. Community structure also clustered in association with the extent of surrounding tree mortality with compositional trends best explained by differences in NH
4
+
concentrations and C/N ratios. C/N ratios, which were lower in soils under beetle-killed trees, further correlated with the relative abundance of putative nitrifiers and exoenzyme activity. Collectively, the response of soil microorganisms that drive heterotrophic respiration and decay supports observations of broader macroscale threshold effects on water quality in heavily infested forests and could be utilized as a predictive mechanism during analogous ecosystem disruptions.

IMPORTANCE
Forests around the world are succumbing to insect infestation with repercussions for local soil biogeochemistry and downstream water quality and quantity. This study utilized microbial community dynamics to address why we are observing watershed scale biogeochemical impacts from forest mortality in some impacted areas but not others. Through a unique “tree-centric” approach, we were able to delineate plots with various tree mortality levels within the same watershed to see if surviving surrounding vegetation altered microbial and biogeochemical responses. Our results suggest that forests with lower overall tree mortality levels are able to maintain “normal” ecosystem function, as the bacterial community appears resistant to tree death. However, surrounding tree mortality influences this mitigating effect with various linear and threshold responses whereupon the bacterial community and its function are altered. Our study lends insight into how microscale responses propagate upward into larger-scale observations, which may be useful for future predictions during analogous disruptions.
Force-Induced Strengthening of the Interaction between
Staphylococcus aureus
Clumping Factor B and Loricrin
Authors: Vitry Pauline , Valotteau Claire , Feuillie Cécile , Bernard Simon , Alsteens David , Geoghegan Joan A. , Dufrêne Yves F.
Published: December 2017

Bacterial pathogens that colonize host surfaces are subjected to physical stresses such as fluid flow and cell surface contacts. How bacteria respond to such mechanical cues is an important yet poorly understood issue.
Staphylococcus aureus
uses a repertoire of surface proteins to resist shear stress during the colonization of host tissues, but whether their adhesive functions can be modulated by physical forces is not known. Here, we show that the interaction of
S. aureus
clumping factor B (ClfB) with the squamous epithelial cell envelope protein loricrin is enhanced by mechanical force. We find that ClfB mediates
S. aureus
adhesion to loricrin through weak and strong molecular interactions both in a laboratory strain and in a clinical isolate. Strong forces (~1,500 pN), among the strongest measured for a receptor-ligand bond, are consistent with a high-affinity “dock, lock, and latch” binding mechanism involving dynamic conformational changes in the adhesin. Notably, we demonstrate that the strength of the ClfB-loricrin bond increases as mechanical force is applied. These findings favor a two-state model whereby bacterial adhesion to loricrin is enhanced through force-induced conformational changes in the ClfB molecule, from a weakly binding folded state to a strongly binding extended state. This force-sensitive mechanism may provide
S. aureus
with a means to finely tune its adhesive properties during the colonization of host surfaces, helping cells to attach firmly under high shear stress and to detach and spread under low shear stress.

IMPORTANCE
Staphylococcus aureus
colonizes the human skin and the nose and can cause various disorders, including superficial skin lesions and invasive infections. During nasal colonization, the
S. aureus
surface protein clumping factor B (ClfB) binds to the squamous epithelial cell envelope protein loricrin, but the molecular interactions involved are poorly understood. Here, we unravel the molecular mechanism guiding the ClfB-loricrin interaction. We show that the ClfB-loricrin bond is remarkably strong, consistent with a high-affinity “dock, lock, and latch” binding mechanism. We discover that the ClfB-loricrin interaction is enhanced under tensile loading, thus providing evidence that the function of an
S. aureus
surface protein can be activated by physical stress.
Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data
Authors: Vital Marius , Karch André , Pieper Dietmar H.
Published: December 2017

Studies focusing on taxonomic compositions of the gut microbiota are plentiful, whereas its functional capabilities are still poorly understood. Specific key functions deserve detailed investigations, as they regulate microbiota-host interactions and promote host health and disease. The production of butyrate is among the top targets since depletion of this microbe-derived metabolite is linked to several emerging noncommunicable diseases and was shown to facilitate establishment of enteric pathogens by disrupting colonization resistance. In this study, we established a workflow to investigate in detail the composition of the polyphyletic butyrate-producing community from omics data extracting its biochemical and taxonomic diversity. By combining information from various publicly available data sets, we identified universal ecological key features of this functional group and shed light on its role in health and disease. Our results will assist the development of precision medicine to combat functional dysbiosis.
On the Power of Uncertainties in Microbial System Modeling: No Need To Hide Them Anymore
Authors: Delahaye Benoit , Eveillard Damien , Bouskill Nicholas
Published: December 2017

For decades, microbiologists have considered uncertainties as an undesired side effect of experimental protocols. As a consequence, standard microbial system modeling strives to hide uncertainties for the sake of deterministic understanding.
PCR detection of segmented filamentous bacteria in the terminal ileum of patients with ulcerative colitis
Authors: Finotti Alessia , Gasparello Jessica , Lampronti Ilaria , Cosenza Lucia Carmela , Maconi Giovanni , Matarese Vincenzo , Gentili Valentina , Di Luca Dario , Gambari Roberto , Caselli Michele
Published: December 2017

Objectives

Segmented filamentous bacteria (SFB) have been detected in a wide range of different animal. Recently, the presence of SFB-like bacteria was shown in biopsies of the terminal ileum and ileocecal valve of both patients with ulcerative colitis and control subjects. The aim of this study was to verify whether PCR methods could be used for the detection of SFB in biopsy of patients with ulcerative colitis and its relationships with the disease stage.

Methods

PCR methods were used to identify SFB in biopsies from the terminal ileum of patients with ulcerative colitis, showing that this approach represents a useful tool for the detection of SFB presence and analysis of the bacterial load.

Results

Our analysis detected SFB in all faecal samples of children at the time of weaning, and also show that putative SFB sequences are present in both patients with ulcerative colitis and control subjects. Results obtained using real-time quantitative PCR analysis confirm the presence of putative SFB sequences in samples from the terminal ileum of patients with ulcerative colitis and in control subjects.

Conclusions

The presence of putative SFB sequence in both patients with ulcerative colitis and control subject suggests that SFB cannot be considered as being uniquely associated with the disease. The second conclusion is that among the patients with ulcerative colitis, a tendency does exist for active disease samples to show higher SFB load, opening new perspectives about possible identification and pharmacological manipulation of SFB-mediated processes for new therapeutic strategy.
Association between individual and neighbourhood socioeconomic factors and masticatory efficiency: a cross-sectional analysis of the Paris Prospective Study 3
Authors: Boillot Adrien , Jouven Xavier , Rangé Hélène , Perier Marie Cécile , Thomas Frédérique , Guibout Catherine , Pannier Bruno , Boutouyrie Pierre , Empana Jean-Philippe , Bouchard Philippe
Published: December 2017

Background

There is a lack of evidence on the impact of socioeconomic factors on masticatory efficiency. The present study investigates the relationship between individual and neighbourhood socioeconomic factors (main exposure) and the number of masticatory units (MUs) used as surrogate of the masticatory efficiency (main outcome).

Methods

In this cross-sectional study nested in the Paris Prospective Study 3, 4270 adults aged 50–75 and recruited from 13 June 2008 to 31 May 2012 underwent a full-mouth examination. Number of MUs defined as pairs of opposing teeth or dental prostheses allowing mastication, number of missing teeth and gingival inflammation were documented. The individual component of the socioeconomic status was evaluated with an individual multidimensional deprivation score and education level. The neighbourhood component of the socioeconomic status was evaluated with the FDep99 deprivation index. Associations were quantified using marginal models.

Results

In multivariate analyses, having less than 5 MUs was associated with (1) the most deprived neighbourhoods (OR=2.27 (95% CI 1.63 to 3.17)), (2) less than 12 years of educational attainment (OR=2.20 (95% CI 1.66 to 2.92)) and (3) the highest individual score of deprivation (OR=3.23 (95% CI 2.24 to 4.65)). Associations with education and individual score of deprivation were consistent across the level of neighbourhood deprivation. Comparable associations were observed with the number of missing teeth. Associations with gingival inflammation were of lower magnitude; the relationship was present for deprivation markers but not for education.

Conclusion

Poor masticatory efficiency is associated with low educational attainment and high deprivation scores.
Modelling the implications of reducing smoking prevalence: the benefits of increasing the UK tobacco duty escalator to public health and economic outcomes
Authors: Knuchel-Takano Andre , Hunt Daniel , Jaccard Abbygail , Bhimjiyani Arti , Brown Martin , Retat Lise , Brown Katrina , Hinde Sebastian , Selvarajah Chit , Bauld Linda , Webber Laura
Published: December 2017

Introduction

Taxing tobacco is one of the most effective ways to reduce smoking prevalence, mitigate its devastating consequential health harms and progress towards a tobacco-free society. This study modelled the health and economic impacts of increasing the existing cigarette tobacco duty escalator (TDE) in the UK from the current 2% above consumer price inflation to 5%.

Methods

A two-stage modelling process was used. First, a non-linear multivariate regression model was fitted to cross-sectional smoking data, creating longitudinal projections from 2015 to 2035. Second, these projections were used to predict the future incidence, prevalence and cost of 17 smoking-related diseases using a Monte Carlo microsimulation approach. A sustained increase in the duty escalator was evaluated against a baseline of continuing historical smoking trends and the existing duty escalator.

Results

A sustained increase in the TDE is projected to reduce adult smoking prevalence to 6% in 2035, from 10% in a baseline scenario. After increasing the TDE, only 65% of female and 60% of male would-be smokers would actually be smoking in 2035. The intervention is projected to avoid around 75 200 new cases of smoking-related diseases between 2015 and 2035. In 2035 alone, £49 m in National Health Service and social care costs and £192 m in societal premature mortality and morbidity costs are projected to be avoided.

Conclusion

Increasing the UK TDE to 5% above inflation could effectively reduce smoking prevalence, prevent diseases and avoid healthcare costs. It would deliver substantial progress towards a tobacco-free society and should be implemented by the UK Government with urgency.
Late Ordovician (Hirnantian) diploporitan fauna of Anticosti Island, Quebec, Canada: implications for evolutionary and biogeographic patterns
Authors: Sheffield Sarah L. , Ausich William I. , Sumrall Colin D.
Published: December 2017

Hirnantian (latest Ordovician) localities containing echinoderm fossils are rare; the few that have been discovered primarily contain disarticulated crinoid ossicles. Therefore, relatively little is known about echinoderm evolutionary dynamics across the Late Ordovician – early Silurian boundary, especially noncrinoid echinoderms. New diploporitan echinoderms, Holocystites salmoensis and an unidentified holocystitid, from reefal facies of the Upper Ordovician Ellis Bay Formation of Anticosti Island provide a critical data point concerning diploporitan biogeography and evolutionary pathways undertaken during the Ordovician and Silurian. These fossils also provide a crucial link in understanding the ancestry of the Silurian Holocystites Fauna, an unusual diploporitan fauna from the middle Silurian of North America, whose origination dates back at least 15 million years earlier than previously thought with the discovery of taxa described here. New fossil data such as these stress the importance of uncovering new localities from underrepresented times and places in Earth’s history, so that these evolutionary transitions can be better understood.