Prototype Variants Research Articles

Calidad física y sensorial del café secado en tres prototipos de secadores solares tipo invernadero

Reducing the drying time of coffee without causing negative effects on cup quality has been the subject of several investigations. The objective was to determine the effect of three variants of a greenhouse-type solar dryer prototype on the physical, sensory and microbiological quality of coffee. The solar dryer prototype with three variants, prototype 1 (P1) greenhouse solar dryer, prototype 2 (P2) solar dryer with air extractor and prototype 3 (P3) solar dryer with air extractor and solar powered heaters, was compared to traditional drying (T0) (cement floor). Drying time, physical grain defects, yield, sensory and microbiological quality were evaluated. The best results were obtained in P3 with a drying time of 52 h (2 ¼ days), with dry parchment coffee beans without primary defects, higher yield in exportable gold coffee (83.24 %), sensory profile of 84.25 points qualified as specialty coffee (with Q Premium grade) and better safety than coffee obtained by traditional drying; demonstrating that the greenhouse type solar dryer with air extractor and solar energy heaters is a sustainable alternative to improve the efficiency of coffee drying while preserving its sensory quality, an essential value for producers to achieve better prices.

Measurements of the flow of a liquid–solid mixture/suspension through a segmented orifice

The paper attempts to solve the metrological problem that occurs when measuring the intensity of a flowing fluid with suspended solids with densities greater and less than the density of the fluid. The issue of the possibility of self-cleaning of a prototype variant of a segmented orifice from floating solid particles forming mixture/suspensions is discussed. For spherical particles of solids calculations have been made to allow for determining a borderline between their floating and entrainment by the flow, based on dimensionless numbers: Archimedes number and Reynolds number. Experimental tests and CFD simulations were conducted with a variable flow determined by Reynolds number for comparable segmental orifices with orifice module m = 0.102. Flow characteristics were plotted. Based on the results obtained from numerical simulations, positive influence of the inclination of skew segmental orifice downflow plane was presented. The results obtained from the study are a guideline for planning further studies to expand the knowledge of segmented orifices with inclined inflow plane.

Reduction of hydrogen absorption into materials of membrane electrode assemblies in hydrogen generators

Objectives. To investigate the possibility of preventing hydrogen absorption into the functional structural materials of hydrogen-generating membrane electrode assemblies based on porous nickel, carbon black, and reduced graphene oxide with platinum–nickel and palladium–nickel nanoparticles.Methods. The hydrogen absorption into materials of membrane electrode assemblies of alkaline electrolyzers was evaluated using an electrolyzer with variable temperature, reagent feed rate, and gas content.Results. The study established the need to use reduced graphene oxide, in order to reduce hydrogen absorption and degradation of hydrogen-generating membrane electrode assemblies.Conclusions. The service life test results and performance of the designed variants of prototypes of membrane electrode assemblies with nanostructured electrodes based on reduced graphene oxide, preventing hydrogen absorption into functional materials and their degradation, demonstrated the creation of hydrogen generators with high energy efficiency shows potential.

T-Cell Exhaustion in HIV-1/Hepatitis C Virus Coinfection Is Reduced After Successful Treatment of Chronic Hepatitis C.

T-cell responses during chronic viral infections become exhausted, which is reflected by upregulation of inhibitory receptors (iRs) and increased interleukin 10 (IL-10). We assessed 2 iRs-PD-1 (programmed cell death protein 1) and Tim-3 (T-cell immunoglobulin and mucin domain-containing protein 3)-and IL-10 mRNAs in peripheral blood mononuclear cells (PBMCs) and their soluble analogs (sPD-1, sTim-3, and IL-10) in plasma in chronic HIV-1/hepatitis C virus (HCV) coinfection and explored the effect of HCV treatment on these markers. We also aimed to establish whether iR expression may be determined by the HCV CD8+ T-cell immunodominant epitope sequence. Plasma and PBMCs from 31 persons with chronic HIV-1/HCV coinfection from the Swiss HIV Cohort Study were collected before and after HCV treatment. As controls, 45 persons who were HIV-1 negative with chronic HCV infection were recruited. Exhaustion markers were assessed by enzyme-linked immunosorbent assay in plasma and by quantitative reverse transcription polymerase chain reaction in PBMCs. Analysis of an HCV epitope sequence was conducted by next-generation sequencing: HLA-A*02-restricted NS31073-1081 and NS31406-1415 and HLA-A*01-restricted NS31436-1444. The study revealed higher plasma sPD-1 (P = .0235) and IL-10 (P = .002) levels and higher IL-10 mRNA in PBMCs (P = .0149) in HIV-1/HCV coinfection. A decrease in plasma sPD-1 (P = .0006), sTim-3 (P = .0136), and IL-10 (P = .0003) and Tim-3 mRNA in PBMCs (P = .0210) was observed following successful HCV treatment. Infection with the HLA-A*01-restricted NS31436-1444 ATDALMTGY prototype variant was related to higher sTim-3 levels than infection with the ATDALMTGF escape variant (P = .0326). The results underscore the synergistic effect of coinfection on expression of exhaustion markers, their reduction following successful HCV treatment and imply that iR levels may operate on an epitope-specific manner.

Comparison of SARS-CoV-2 entry inhibitors based on ACE2 receptor or engineered Spike-binding peptides.

With increasing resistance of SARS-CoV-2 variants to antibodies, there is interest in developing entry inhibitors that target essential receptor-binding regions of the viral Spike protein and thereby present a high bar for viral resistance. Such inhibitors could be derivatives of the viral receptor, ACE2, or peptides engineered to interact specifically with the Spike receptor-binding pocket. We compared the efficacy of a series of both types of entry inhibitors, constructed as fusions to an antibody Fc domain. Such a design can increase protein stability and act to both neutralize free virus and recruit effector functions to clear infected cells. We tested the reagents against prototype variants of SARS-CoV-2, using both Spike pseudotyped vesicular stomatitis virus vectors and replication-competent viruses. These analyses revealed that an optimized ACE2 derivative could neutralize all variants we tested with high efficacy. In contrast, the Spike-binding peptides had varying activities against different variants, with resistance observed in the Spike proteins from Beta, Gamma, and Omicron (BA.1 and BA.5). The resistance mapped to mutations at Spike residues K417 and N501 and could be overcome for one of the peptides by linking two copies in tandem, effectively creating a tetrameric reagent in the Fc fusion. Finally, both the optimized ACE2 and tetrameric peptide inhibitors provided some protection to human ACE2 transgenic mice challenged with the SARS-CoV-2 Delta variant, which typically causes death in this model within 7-9 days. IMPORTANCE The increasing resistance of SARS-CoV-2 variants to therapeutic antibodies has highlighted the need for new treatment options, especially in individuals who do not respond to vaccination. Receptor decoys that block viral entry are an attractive approach because of the presumed high bar to developing viral resistance. Here, we compare two entry inhibitors based on derivatives of the ACE2 receptor, or engineered peptides that bind to the receptor-binding pocket of the SARS-CoV-2 Spike protein. In each case, the inhibitors were fused to immunoglobulin Fc domains, which can further enhance therapeutic properties, and compared for activity against different SARS-CoV-2 variants. Potent inhibition against multiple SARS-CoV-2 variants was demonstrated in vitro, and even relatively low single doses of optimized reagents provided some protection in a mouse model, confirming their potential as an alternative to antibody therapies.

Magnetostrictive Fiber Sensors as Total Field Magnetometers

A novel magnetostrictive thin film fiber sensor is presented which can be utilized in an interferometric architecture. The magnetostrictive fiber sensor utilizes novel fiber and thin film technology to achieve high sensitivity in the sub-nanotesla regime. The base sensor architecture utilizes optical fiber wound in a novel low stress flat coil resembling a record, coated with a thin magnetostrictive film. Two prototype variants were fabricated, incorporating FeCo sputtered films of different thicknesses on 4 μm polyimide jacket single mode fiber. The sensors were incorporated into a fiber optic interferometric measurement apparatus to characterize time-varying magnetic field sensitivity. Device results are presented which demonstrate sensitivity is a function of film thickness. The experimental data exhibited a two-order magnitude sensitivity improvement as the thin film thickness was doubled. Sensitivity projections are made based on film thickness.

Optimization of sound insulation of flat panel photobioreactors for bioenergy facades

Flat panel photobioreactors consisting of different layers of glass panes, designed to allow heat and microalgae biomass production in a water layer by solar radiation at the facade of buildings (i.e. bioenergy facade), were acoustically examined and further developed for increased sound insulation against external noise exposure. The sound insulation was first examined by simulations on double-, triple- and four-skin bioreactor variants. Parameters such as the distance between panes, the number and types of layers, as well as the material and thickness of the glass panes, were varied. Especially the influence of decoupling layers and an airlift on the sound reduction index was evaluated. Based on the simulation results, a modular prototype was developed which could be converted into a double-, triple- or four-skin structure as required. The sound reduction of these was studied in an acoustic window laboratory experimentally. The highest measured weighted sound reduction index of 51 dB was obtained with a four-skin photobioreactor variant with four glass pane layers and a water layer. The weighted sound reduction indexes for alternative four-skin opaque prototype variants with a plasterboard layer were 2—3 dB lower. The double- and triple-skin variants achieved 43—47 dB. The use of XPS as insulation material in the outer air layers of the triple- and four-skin variants reduced the weighted sound reduction index by 2 dB. The airlift needed for turbulent mixing of the microalgae had no effect on the sound insulation but increased the average ambient noise level by up to 10 dB. With 51 dB, the four-shell photobioreactor prototype achieves sound insulation class 5 according to the german regulation VDI 2719 for windows and thus fulfills the function of a sound insulation element in the facade of buildings or in a soundproof wall.

GSMFlow: Generation Shifts Mitigating Flow for Generalized Zero-Shot Learning

Generalized Zero-Shot Learning (GZSL) aims to recognize images not only for seen classes but also for unseen ones by transferring semantic-visual relationships from the seen to the unseen classes. It is an intuitive solution to take the advantage of generative models to hallucinate realistic unseen samples based on the knowledge learned from the seen classes. However, due to the generation shifts, the synthesized samples by most existing methods may drift from the real distribution of the unseen data. To address this issue, we propose a novel flow-based generative framework that consists of multiple conditional affine coupling layers for learning unseen data generation. Specifically, we investigate and address three essential problems that trigger the generation shifts, <i>i.e.</i>, <i>semantic inconsistency</i>, <i>variance collapse</i>, and <i>structure disorder</i>. First, to improve the reflection of the semantic information in the generated samples, we proactively embed the semantic information into the transformation in each conditional affine coupling layer. Second, to promote the intrinsic feature variance of the unseen classes, we introduce a boundary sample mining strategy with entropy maximization to discover ambiguous visual variants of semantic prototypes and hereby calibrate the decision boundary of the classifiers. Third, a relative positioning strategy is proposed to revise the attribute embeddings, guiding which to fully preserve the inter-class geometric structure and further avoid structure disorder in the semantic space. Extensive experimental results on four GZSL benchmark datasets demonstrate that GSMFlow achieves the state-of-the-art performance on GZSL.

Агентно-ориентированный подход к проектированию гибких производственных систем

The article considers the process of designing modules of a flexible production site using multi-agent technology. For a comprehensive organization of the design, there has been proposed an algorithm of intelligent automated design of the complex technical systems, flexible manufacture systems (FMS) being used as an example. It has been stated that the research at the stages of the conceptual design of the FMS is carried out by collecting prototype variants with using expert knowledge and interaction of agents-designers according to the method of self-realizing computer aided design. Building a distributed system for the intelligent design of a hybrid architecture using the features of agent technology is considered. A flexible manufacture system is chosen as a design object, which is a complex technical object of research, the process of its design is multi-stage and iterative. To design such systems using a common functional model at the initial stage, a set of tasks is defined to facilitate the computing design of the FMS. This approach to the design of FMS requires implementing the solutions of a large number of local problems of different purposes. To solve the local problems of design procedures there has been proposed a multi-agent design technology, where the agent-designer performs a specific local task of the design process. The developed formalisms and algorithms help automate the synthesis of technical objects of the FMS. To build an automated conceptual design system as main decision-making for the multi-agent systems, there has been proposed a technical solution based on the knowledge of intelligent multi-agent systems. Using a multi-agent system makes it possible to build a distributed parallel design system with ability to be transferred to various hardware and software platforms. There has been also proposed the structure of a multi-agent system for the intelligent computer-aided design based on the designer's knowledge base.

Development of blood hemoglobin level early detection device based on a noninvasive optical platform

Blood hemoglobin levels are a reliable indicator for anemia screening, which generally uses an invasive system or takes blood using a syringe. Spectrophotometry can work by “substituting” the use of a phlebotomy tube needle with electromagnetic wave radiation or light. This study aims to develop and carry out a noninvasive diagnostic test for measuring hemoglobin levels. There are three main stages in this research: (i) measuring hemoglobin concentration and scanning an incident wavelength on standard hemoglobin solutions and blood controls, (ii) making a prototype variant of a noninvasive blood hemoglobin level measurement device, and (iii) testing the technology unit on the developed prototype. The measured hemoglobin value by the Trax Control Meter for low, middle, and high levels is almost the same as the expected range values, namely, 13.09, 16.8, and 17.81 g/dL, respectively. Three sets of device prototype variants were successfully developed: (i) the noninvasive blood hemoglobin level measuring device based on Raspberry Pi Prototype on Infant Finger and Thigh Probes, (ii) the level measuring prototype noninvasive hemoglobin in blood based on Internet of Things and WebServer, and (iii) the prototype of noninvasive blood hemoglobin level measuring device on in vitro probe with reflectance method. Testing the accuracy of the Biorad MeterTrax Trilevel using a multiformula regression calculation using the ZunZun server shows that the tool has an accuracy ranging from 0.12 to 0.30 g/dL.

A protein A based Staphylococcus aureus vaccine with improved safety

Exposure to Staphylococcus aureus does not lead to immunity as evidenced by the persistent colonization of one third of the human population. S. aureus immune escape is mediated by factors that preempt complement activation, destroy phagocytes, and modify B and T cell responses. One such factor, Staphylococcal protein A (SpA) encompasses five Immunoglobulin binding domains (IgBDs) that associate with the Fcγ domain to block phagocytosis. IgBDs also associate with Fab encoded by VH3 clan related genes. SpA binding to VH3-IgM that serves as a B cell receptor results in B cell expansion and secretion of antibodies with no specificity for S. aureus. SpA crosslinking of VH3-IgG and VH3-IgE bound to cognate receptors of mast cells and basophils promotes histamine release and anaphylaxis. Earlier work developed a prototype variant SpAKKAA with four amino acid substitutions in each IgBD. When tested in animal models, SpAKKAA elicited neutralizing antibodies and protection against infection. We show here that SpAKKAA retains crosslinking activity for VH3-IgG and VH3-IgE. We use a rational approach to design and test 67 new SpA variants for loss of VH3 binding and anaphylactic activities. We identify two detoxified candidates that elicit SpA-neutralizing antibodies and protect animals from S. aureus colonization and bloodstream infection. The new detoxified SpA candidates bear three instead of four amino acid substitutions thus increasing the development of SpA-specific antibodies. We propose that detoxified SpA variants unable to crosslink VH3-idiotypic immunoglobulin may be suitably developed as clinical-grade vaccines for safety and efficacy testing in humans.

Innovative Conceptual Design for Patentability. Case Study of the Double Compartment Thermos Container

Abstract Any initial product started from a more or less flexible idea, or a patented idea transposed into a manufactured product. This idea takes a new development following the study of the marketing market, analysis studies and all we need for technological opportunity, outlining at the same time stage by stage the prototype concept. The prototype variant is again subjected to a systemic analysis that defines and optimizes the final product, as well as the technological flow associated with the entire manufacturing process applied on the concept. The paper proposes a synthesis analysis on innovative conceptual design. The case study presented in this paper shows a reserch study applied on the industrial product for which the patent was obtained, respectively a double compartmented thermos container [17].

Geometry of Ancient Mazes: A Synthesis Part II: ‘Roman’ Mazes

The aim of the present survey was an investigation of the processes implemented for conceiving and setting up three types of ancient mazes which have come down to us on various media (stone, mosaic, painting, ceramic, coins…) from Prehistory to Middle Ages (and, for some, even later). The first part of this study was devoted to the so-called ‘Cretan’ mazes, and this second part focusses on a corpus of 43 ‘Roman’ mazes ranging from Portugal and England to Cyprus and from 100 BC to AD 330. Like the other one, this type is well individualized and homogeneous; it is characterized by several similar sectors run through, clockwise or anticlockwise. An introductory study of a maze exemplifies the fundamental duality between path and walls and the various types of meanders which are to be met with. Then a general processes for setting up a Roman maze, beginning with making a regular grid, going on with filling a sector and duplicating it and ending with managing an entrance/exit device, is proposed. Variants of the general prototype are also reviewed. In particular, in the course of this work a comparative study enabled to investigate the complex and intriguing maze of Pula (Croatia), the structure of which can now be better understood.

Enhancement of solute clearance using pulsatile push-pull dialysate flow for the Quanta SC+: A novel clinic-to-home haemodialysis system.

The SC+ haemodialysis system developed by Quanta Dialysis Technologies is a small, easy-to-use dialysis system designed to improve patient access to self-care and home haemodialysis. A prototype variant of the standard SC+ device with a modified fluidic management system generating a pulsatile push-pull dialysate flow through the dialyser during use has been developed for evaluation. It was hypothesized that, as a consequence of the pulsatile push-pull flow through the dialyser, the boundary layers at the membrane surface would be disrupted, thereby enhancing solute transport across the membrane, modifying protein fouling and maintaining the surface area available for mass and fluid transport throughout the whole treatment, leading to solute transport (clearance) enhancement compared to normal haemodialysis (HD) operation. The pumping action of the SC+ system was modified by altering the sequence and timings of the valves and pumps associated with the flow balancing chambers that push and pull dialysis fluid to and from the dialyser. Using this unique prototype device, solute clearance performance was assessed across a range of molecular weights in two related series of laboratory bench studies. The first measured dialysis fluid moving across the dialyser membrane using ultrasonic flowmeters to establish the validity of the approach; solute clearance was subsequently measured using fluorescently tagged dextran molecules as surrogates for uraemic toxins. The second study used human blood doped with uraemic toxins collected from the spent dialysate of dialysis patients to quantify solute transport. In both, the performance of the SC+ prototype was assessed alongside reference devices operating in HD and pre-dilution haemodiafiltration (HDF) modes. Initial testing with fluorescein-tagged dextran molecules (0.3 kDa, 4 kDa, 10 kDa and 20 kDa) established the validity of the experimental pulsatile push-pull operation in the SC+ system to enhance clearance and demonstrated a 10 to 15% improvement above the current HD mode used in clinic today. The magnitude of the observed enhancement compared favourably with that achieved using pre-dilution HDF with a substitution fluid flow rate of 60 mL/min (equivalent to a substitution volume of 14.4 L in a 4-hour session) with the same dialyser and marker molecules. Additional testing using human blood indicated a comparable performance to pre-dilution HDF; however, in contrast with HDF, which demonstrated a gradual decrease in solute removal, the clearance values using the pulsatile push-pull method on the SC+ system were maintained over the entire duration of treatment. Overall albumin losses were not different. Results obtained using an experimental pulsatile push-pull dialysis flow configuration with an aqueous blood analogue and human blood ex vivo demonstrate an enhancement of solute transport across the dialyser membrane. The level of enhancement makes this approach comparable with that achieved using pre-dilution HDF with a substitution fluid flow rate of 60 mL/min (equivalent to a substitution volume of 14.4 L in a 4-hour session). The observed enhancement of solute transport is attributed to the disruption of the boundary layers at the fluid-membrane interface which, when used with blood, minimizes protein fouling and maintains the surface area.

Efficient reordered nonlinear Gauss–Seidel solvers with higher order for black-oil models

The fully implicit method is the most commonly used approach to solve black-oil problems in reservoir simulation. The method requires repeated linearization of large nonlinear systems and produces ill-condi\-tioned linear systems. We present a strategy to reduce computational time that relies on two key ideas: (\textit{i}) a sequential formulation that decouples flow and transport into separate subproblems, and (\textit{ii}) a highly efficient Gauss--Seidel solver for the transport problems. This solver uses intercell fluxes to reorder the grid cells according to their upstream neighbors, and groups cells that are mutually dependent because of counter-current flow into local clusters. The cells and local clusters can then be solved in sequence, starting from the inflow and moving gradually downstream, since each new cell or local cluster will only depend on upstream neighbors that have already been computed. Altogether, this gives optimal localization and control of the nonlinear solution process. This method has been successfully applied to real-field problems using the standard first-order finite volume discretization. Here, we extend the idea to first-order dG methods on fully unstructured grids. We also demonstrate proof of concept for the reordering idea by applying it to the full simulation model of the Norne oil field, using a prototype variant of the open-source OPM Flow simulator.

Feature-Based Response Classification in Nonlinear Structural Design Simulations

An applied system design analysis approach for automated processing and classification of simulated structural responses is presented. Deterministic and nonlinear dynamics are studied under ideal loading and low noise conditions to determine fundamental system properties, how they vary and possibly interact. Using powerful computer resources, large amounts of simulated raw data can be produced in a short period of time. Efficient tools for data processing and interpretation are then needed, but existing ones often require much manual preparation and direct human judgement. Thus, there is a need to develop techniques that help to treat more virtual prototype variants and efficiently extract useful information from them. For this, time signals are evaluated by methods commonly used within structural dynamics and statistical learning. A multi-level multi-frequency stimulus function is constructed and simulated response signals are combined into frequency domain functions. These are associated with qualitative system features, such as being periodic or aperiodic, linear or nonlinear and further into subcategories of nonlinear systems, such as fundamental, sub or super harmonic and even or odd order types. Appropriate classes are then determined from selected feature metrics and rules-of-thumb criteria. To automate the classification of large data sets, a support vector machine is trained on categorised responses to determine whether a single feature, or combinations of features, applies or not. The trained classifier can then efficiently process new sets of data and pick out cases that are associated with possible vibrational problems, which subsequently can be further analysed and understood. This article describes elements of the analysis, discuss the effectiveness of evaluated feature metrics, reports practical considerations and results from two separate training study examples.

Building community-driven vertical greening systems for people living on less than £1 a day: A case study in Nigeria

This paper reports and evaluates the process involved in designing and building affordable community-driven vertical greening systems (VGS) prototypes in a low-income neighbourhood of Lagos, Nigeria. Prototypes are intended to fulfil the dual function of improving indoor thermal comfort conditions and providing substrate to grow edible and medicinal plants. Besides that, the research aims to identify entrepreneurial competences and relationships in the community to transform the prototypes into commercially viable local products. ‘Qualitative fieldwork’ is used as a methodological approach and a product development roadmap is proposed that reports: design and construction development; performance evaluation of thermal impact and plant growth; costing; and community acceptability of the four different prototypes built in two different phases: rainy season 2014 and dry season 2016. The prototypes reduced internal air temperatures by an average of 2.3 °C, moving internal comfort conditions to the comfort zone for around 90%–100% of the time. Besides that, they provided around 16 crops of edible and medicinal plants per year. For two variants of prototypes (bamboo and prefabricated timber), the study reports a range of revenues from the sales of crops, and the estimated payback period (PBP) and internal rate of return (IRR) of the investment.

A Case Study on Iteratively Assessing and Enhancing Wearable User Interface Prototypes

Wearable devices are being explored and investigated as a promising computing platform as well as a source of personal big data for the post smartphone era. To deal with a series of rapidly developed wearable prototypes, a well-structured strategy is required to assess the prototypes at various development stages. In this paper, we first design and develop variants of advanced wearable user interface prototypes, including joystick-embedded, potentiometer-embedded, motion-gesture and contactless infrared user interfaces for rapidly assessing hands-on user experience of potential futuristic user interfaces. To achieve this goal systematically, we propose a conceptual test framework and present a case study of using the proposed framework in an iterative cyclic process to prototype, test, analyze, and refine the wearable user interface prototypes. We attempt to improve the usability of the user interface prototypes by integrating initial user feedback into the leading phase of the test framework. In the following phase of the test framework, we track signs of improvements through the overall results of usability assessments, task workload assessments and user experience evaluation of the prototypes. The presented comprehensive and in-depth case study demonstrates that the iterative approach employed by the test framework was effective in assessing and enhancing the prototypes, as well as gaining insights on potential applications and establishing practical guidelines for effective and usable wearable user interface development.

Erratum to: Functional variants of human papillomavirus type 16 demonstrate host genome integration and transcriptional alterations corresponding to their unique cancer epidemiology.

Human papillomaviruses (HPVs) are a worldwide burden as they are a widespread group of tumour viruses in humans. Having a tropism for mucosal tissues, high-risk HPVs are detected in nearly all cervical cancers. HPV16 is the most common high-risk type but not all women infected with high-risk HPV develop a malignant tumour. Likely relevant, HPV genomes are polymorphic and some HPV16 single nucleotide polymorphisms (SNPs) are under evolutionary constraint instigating variable oncogenicity and immunogenicity in the infected host. To investigate the tumourigenicity of two common HPV16 variants, we used our recently developed, three-dimensional organotypic model reminiscent of the natural HPV infectious cycle and conducted various “omics” and bioinformatics approaches. Based on epidemiological studies we chose to examine the HPV16 Asian-American (AA) and HPV16 European Prototype (EP) variants. They differ by three non-synonymous SNPs in the transforming and virus-encoded E6 oncogene where AAE6 is classified as a high- and EPE6 as a low-risk variant. Remarkably, the high-risk AAE6 variant genome integrated into the host DNA, while the low-risk EPE6 variant genome remained episomal as evidenced by highly sensitive Capt-HPV sequencing. RNA-seq experiments showed that the truncated form of AAE6, integrated in chromosome 5q32, produced a local gene over-expression and a large variety of viral-human fusion transcripts, including long distance spliced transcripts. In addition, differential enrichment of host cell pathways was observed between both HPV16 E6 variant-containing epithelia. Finally, in the high-risk variant, we detected a molecular signature of host chromosomal instability, a common property of cancer cells. We show how naturally occurring SNPs in the HPV16 E6 oncogene cause significant changes in the outcome of HPV infections and subsequent viral and host transcriptome alterations prone to drive carcinogenesis. Host genome instability is closely linked to viral integration into the host genome of HPV-infected cells, which is a key phenomenon for malignant cellular transformation and the reason for uncontrolled E6 oncogene expression. In particular, the finding of variant-specific integration potential represents a new paradigm in HPV variant biology.

Functional variants of human papillomavirus type 16 demonstrate host genome integration and transcriptional alterations corresponding to their unique cancer epidemiology.

BackgroundHuman papillomaviruses (HPVs) are a worldwide burden as they are a widespread group of tumour viruses in humans. Having a tropism for mucosal tissues, high-risk HPVs are detected in nearly all cervical cancers. HPV16 is the most common high-risk type but not all women infected with high-risk HPV develop a malignant tumour. Likely relevant, HPV genomes are polymorphic and some HPV16 single nucleotide polymorphisms (SNPs) are under evolutionary constraint instigating variable oncogenicity and immunogenicity in the infected host.ResultsTo investigate the tumourigenicity of two common HPV16 variants, we used our recently developed, three-dimensional organotypic model reminiscent of the natural HPV infectious cycle and conducted various “omics” and bioinformatics approaches. Based on epidemiological studies we chose to examine the HPV16 Asian-American (AA) and HPV16 European Prototype (EP) variants. They differ by three non-synonymous SNPs in the transforming and virus-encoded E6 oncogene where AAE6 is classified as a high- and EPE6 as a low-risk variant. Remarkably, the high-risk AAE6 variant genome integrated into the host DNA, while the low-risk EPE6 variant genome remained episomal as evidenced by highly sensitive Capt-HPV sequencing. RNA-seq experiments showed that the truncated form of AAE6, integrated in chromosome 5q32, produced a local gene over-expression and a large variety of viral-human fusion transcripts, including long distance spliced transcripts. In addition, differential enrichment of host cell pathways was observed between both HPV16 E6 variant-containing epithelia. Finally, in the high-risk variant, we detected a molecular signature of host chromosomal instability, a common property of cancer cells.ConclusionsWe show how naturally occurring SNPs in the HPV16 E6 oncogene cause significant changes in the outcome of HPV infections and subsequent viral and host transcriptome alterations prone to drive carcinogenesis. Host genome instability is closely linked to viral integration into the host genome of HPV-infected cells, which is a key phenomenon for malignant cellular transformation and the reason for uncontrolled E6 oncogene expression. In particular, the finding of variant-specific integration potential represents a new paradigm in HPV variant biology.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3203-3) contains supplementary material, which is available to authorized users.