Miracle-dz/UniFAR-FTUs huggingface dataset:
Retroviral Antisense Transcripts and Genes: 33 Years after First Predicted, a Silent Retroviral Revolution?

Paradigm shifts throughout the history of microbiology have typically been ignored, or met with skepticism and resistance, by the scientific community. This has been especially true in the field of virology, where the discovery of a “contagium vivum fluidum”, or infectious fluid remaining after excluding bacteria by filtration, was initially ignored because it did not coincide with the established view of microorganisms. Subsequent studies on such infectious agents, eventually termed “viruses”, were met with skepticism. However, after an abundance of proof accumulated, viruses were eventually acknowledged as defined microbiological entities. Next, the proposed role of viruses in oncogenesis in animals was disputed, as was the unique mechanism of genome replication by reverse transcription of RNA by the retroviruses. This same pattern of skepticism holds true for the prediction of the existence of retroviral “antisense” transcripts and genes. From the time of their discovery, it was thought that retroviruses encoded proteins on only one strand of proviral DNA. However, in 1988, it was predicted that human immunodeficiency virus type 1 (HIV-1), and other retroviruses, express an antisense protein encoded on the DNA strand opposite that encoding the known viral proteins. Confirmation came quickly with the characterization of the antisense protein, HBZ, of the human T-cell leukemia virus type 1 (HTLV-1), and the finding that both the protein and its antisense mRNA transcript play key roles in viral replication and pathogenesis. However, acceptance of the existence, and potential importance, of a corresponding antisense transcript and protein (ASP) in HIV-1 infection and pathogenesis has lagged, despite gradually accumulating theoretical and experimental evidence. The most striking theoretical evidence is the finding that asp is highly conserved in group M viruses and correlates exclusively with subtypes, or clades, responsible for the AIDS pandemic. This review outlines the history of the major shifts in thought pertaining to the nature and characteristics of viruses, and in particular retroviruses, and details the development of the hypothesis that retroviral antisense transcripts and genes exist. We conclude that there is a need to accelerate studies on ASP, and its transcript(s), with the view that both may be important, and overlooked, targets in anti-HIV therapeutic and vaccine strategies.
Fundamental mode estimation for modern cable-stayed bridges considering the tower flexibility

The design of cable-stayed bridges is typically governed by the dynamic response. This work provides designers with essential information about the fundamental vibration modes, proposing analytical expressions based on the mechanical and geometrical properties of the structure. Different bridge geometries are usually considered in the early design stages until the optimum solution is defined. In these design stages, the analytical formulation is advantageous, because finite-element models are not required and modifying the bridge characteristics is straightforward. The influence of the tower flexibility is included in this study, unlike in previous attempts on mode estimation. The dimensions and proportions of the canonical models proposed in the analytical study stem from the previous compilation of the dimensions of a large number of constructed cable-stayed bridges. Five tower shapes, central or lateral cable-system layouts and box- or U-shaped deck sections, have been considered. The vibration properties of more than 1,000 cable-stayed bridges with main spans ranging from 200 to 800 m long were extracted within an extensive parametric analysis. The Vaschy-Buckingham theorem of dimensional analysis was applied to the numerical results to propose the formulation for period estimation. Finally, the formulas were validated with the vibration properties of 17 real cable-stayed bridges constructed in different countries. The importance of the tower flexibility is verified, and the errors observed are typically below 15%, significantly improving the estimations obtained by previous research works.
International Workshop on Automobile , Power and Energy Engineering Study of Drain Induced Barrier Lowering ( DIBL ) Effect for Strained Si nMOSFET

Drain Induced Barrier Lowering(DIBL) effect is prominent as the feature size of MOS device keep diminishing. In this paper, a threshold voltage model for small-scaled strained Si nMOSFET is proposed to illustrate the DIBL effect, which is based on solving 2-D Poisson equation. By simulation, the relationship between DIBL and channel length, gate oxide thickness, Ge content, and channel doping concentration has been analyzed and the way to restrain the DIBL effect has been acquired. By using ISETCAD device simulator, the validity of the model has also been proved. © 2010 Published by Elsevier Ltd. Selection and/or peer-review under responsibility of Society for Automobile, Power and Energy Engineering
Biological and Mechanical Characterization of the Random Positioning Machine (RPM) for Microgravity Simulations

The rapid improvement of space technologies is leading to the continuous increase of space missions that will soon bring humans back to the Moon and, in the coming future, toward longer interplanetary missions such as the one to Mars. The idea of living in space is charming and fascinating; however, the space environment is a harsh place to host human life and exposes the crew to many physical challenges. The absence of gravity experienced in space affects many aspects of human biology and can be reproduced in vitro with the help of microgravity simulators. Simulated microgravity (s-μg) is applied in many fields of research, ranging from cell biology to physics, including cancer biology. In our study, we aimed to characterize, at the biological and mechanical level, a Random Positioning Machine in order to simulate microgravity in an in vitro model of Triple-Negative Breast Cancer (TNBC). We investigated the effects played by s-μg by analyzing the change of expression of some genes that drive proliferation, survival, cell death, cancer stemness, and metastasis in the human MDA-MB-231 cell line. Besides the mechanical verification of the RPM used in our studies, our biological findings highlighted the impact of s-μg and its putative involvement in cancer progression.
Guest Editorial - Special Issue on Internet of Things (IoT): Architecture, Protocols and Services

The internet of things (IoT) has been emerging as the next big 'thing' in Internet. It is envisioned that billions of physical things or objects will be outfitted with different kinds of sensors and actuators and connected to the Internet via heterogeneous access networks enabled by technologies such as embedded sensing and actuating, radio frequency identification (RFID), wireless sensor networks, real-time and semantic web services, etc. IoT is actually cyber-physical systems or a network of networks. With the huge number of things/objects and sensors/actuators connected to the Internet, a massive and in some cases real-time data flow will be automatically produced by connected things and sensors. It is important to collect correct raw data in an efficient way; but more important is to analyze and mine the raw data to abstract more valuable information such as correlations among things and services to provide web of things or Internet of services. This special issue features recent and emerging advances IoT architecture, protocols, services and applications. More than one hundred papers were received and peer-reviewed, out of which thirty five papers were selected for publication, which cover topics including sensors and devices for IoT, efficient communications and networking for IoT, security and privacy in IoT, crowdsensing and crowdsourcing, localization and tracking, services and applications, and IoT data modeling and management. The first set of five papers discuss IoT sensor and device related issues. The second set includes fourteen papers about efficient communications and networking for IoT. Security and privacy is another important aspect in IoT. Five papers focusing on IoT security and privacy were selected. Four papers concentrating on tracking and localization were selected and three more papers about IoT data modeling and management were included in this special issue. Finally, there were three papers which presented new IoT services and applications.
Numerical modeling of volatile organic compound emissions from ozone reactions with human-worn clothing in an aircraft cabin

Volatile organic compounds are indoor air pollutants with many adverse health effects for humans. Ozone reactions with human surfaces (skin, hair, and clothing) are an important source of volatile organic compounds in the indoor air, especially in aircraft cabins because of their typically high ozone concentrations and occupant densities. Therefore, it is important to study the ozone-initiated volatile organic compound emissions from ozone reactions with passengers in an aircraft cabin and assess their resulting exposure. This investigation developed empirical models for computing the emissions of several major volatile organic compounds, including acetone, 4-oxopentanal, nonanal, and decanal, from ozone reactions with human-worn clothing. The empirical models were used to compute the contributions of human surfaces to these volatile organic compounds in an aircraft cabin mockup under different environmental conditions. The computed results were then compared with the corresponding experimental data obtained in the mockup. The models can provide rough estimates of ozone-initiated volatile organic compound concentrations. The empirical models were integrated into a computational fluid dynamics analysis, and the results showed that the levels of ozone-initiated volatile organic compounds were significantly enhanced in the breathing zones of the passengers. Therefore, to accurately assess passenger exposure to volatile organic compounds, their concentrations in the breathing zones should be used.
Monitoring of Laminated Composites Delamination Based on Electro-Mechanical Impedance Measurement

This paper paves the way for a multi-damage monitoring system for composite structures. The final goal of this work being to design a monitoring system able to predict the damage in the composite structure under static and fatigue loading. This system will be based on the simultaneous use of measurement and damage predicting models. We describe the first step of this work, which consists in the use of electro-mechanical impedance measurement to detect delamination. An electro-mechanical model of a beam into which delamination has been introduced is presented and compared with experimental results. The influence of geometrical parameters is studied and future improvements of our method are outlined.
Modelling reconfigurable manufacturing systems with coloured timed Petri nets

Reconfigurable manufacturing systems (RMSs) have been acknowledged as a promising means of providing manufacturing companies with the required production capacities and capabilities. This is accomplished through reconfiguring system elements over time for a diverse set of individualised products often required in small quantities and with short delivery lead times. Recognising the importance of dynamic modelling and visualisation in decision-making support in RMSs and the limitations of current research, we propose in this paper to model RMSs with Petri net (PN) techniques with focus on the process of reconfiguring system elements while considering constraints and system performance. In view of the modelling challenges, including variety handling, production variation accommodation, machine selection, and constraint satisfaction, we develop a new formalism of coloured timed PNs. In conjunction with coloured tokens and timing in coloured and timed PNs, we also define a reconfiguration mechanism to meet modelling challenges. An application case from an electronics company producing mobile phone vibration motors is presented. Also reported are system analysis and application results, which show how the proposed formalism can be used in the reconfiguration decision making process.
Single-Cell RNA Sequencing Reveals Heterogeneity and Functional Diversity of Lymphatic Endothelial Cells

Lymphatic endothelial cells (LECs) line the lymphatic vasculature and play a central role in the immune response. LECs have abilities to regulate immune transport, to promote immune cell survival, and to cross present antigens to dendritic cells. Single-cell RNA sequencing (scRNA) technology has accelerated new discoveries in the field of lymphatic vascular biology. This review will summarize these new findings in regard to embryonic development, LEC heterogeneity with associated functional diversity, and interactions with other cells. Depending on the organ, location in the lymphatic vascular tree, and micro-environmental conditions, LECs feature unique properties and tasks. Furthermore, adjacent stromal cells need the support of LECs for fulfilling their tasks in the immune response, such as immune cell transport and antigen presentation. Although aberrant lymphatic vasculature has been observed in a number of chronic inflammatory diseases, the knowledge on LEC heterogeneity and functional diversity in these diseases is limited. Combining scRNA sequencing data with imaging and more in-depth functional experiments will advance our knowledge of LECs in health and disease. Building the case, the LEC could be put forward as a new therapeutic target in chronic inflammatory diseases, counterweighting the current immune-cell focused therapies.
Investigation on the RESET switching mechanism of bipolar Cu/HfO2/Pt RRAM devices with a statistical methodology

The RESET switching of bipolar Cu/HfO2/Pt resistance random access memory (RRAM) is investigated. With a statistical methodology, we systematically analyze the RESET voltage (VRESET) and RESET current (IRESET). VRESET shows a U-shape distribution as a function of RON according to the scatter plot of the raw experimental data. After data correction by a series resistance (RS), VRESET is nearly constant, while IRESET decreases linearly with RCF. These behaviours are consistent with the thermal dissolution model of RESET. Moreover, the IRESET and VRESET distributions are strongly affected by the RON distribution. Using a ‘resistance screening’ method, the IRESET and VRESET distributions are found to be compatible with the Weibull distribution model. The Weibull slopes of the VRESET and IRESET distributions are independent of RCF, indicating that the RESET point corresponds to the initial phase of conductive filament (CF) dissolution, according to our cell-based model for the unipolar RESET of RRAM devices. The scale factor of the VRESET distributions is roughly constant, while that of the IRESET distributions scale with 1/RCF. Accordingly, the RESET switching of the HfO2-based solid electrolyte memory is compatible with the thermal dissolution mechanism, improving our understanding on the physics of resistive switching of RRAM devices.
Influence of Potential Function Asymmetries on the Performance of Nonlinear Energy Harvesters Under White Noise

To improve the broadband transduction capabilities of vibratory energy harvesters (VEHs) under random and non-stationary excitations, many researchers have resorted to purposefully introducing nonlinearities into the restoring force of the harvester. While performing this task, it is often very challenging to maintain a perfectly symmetric restoring force which usually yields a VEH with an asymmetric potential energy function. This paper investigates the influence of potential function asymmetries on the performance of nonlinear VEHs under white noise inputs. To that end, a quadratic nonlinearity is introduced into the restoring force of the harvester and its influence on the mean power for both mono- and bi-stable potentials is investigated. It is shown that, for VEHs with a mono-stable potential function, the mean output power increases with the degree of potential function asymmetry. On the other hand, for energy harvesters with a bi-stable potential function, asymmetries in the restoring force appear to worsen performance especially for low to moderate noise intensities. When the noise intensity becomes sufficiently large, the influence of the potential function’s asymmetry on the mean power diminishes. Results also reveal that a VEH with a symmetric bi-stable potential function produces higher mean power levels than the one with the most asymmetric mono-stable potential. As such, it is concluded that a VEH with a bi-stable symmetric potential is most desirable to improve performance under white noise.Copyright © 2014 by ASME
Smallholding farmers’ resilience towards economic and ecological disruption of oil palm plantations

Indonesian smallholder oil palm plantations are facing both economic and ecological challenges, therefore the farmers struggle to be resilient. This study constructs two purposes, (1) to measure the resilience level of smallholder plantations, and (2) to assess the effect of economic and ecological disruption on smallholders’ resilience. We interviewed a sample of 120 smallholders in South Bengkulu regency, Bengkulu Province, Indonesia. The methodology deploys a quantitative method (statistics and econometrics) to analyze the effect of disruptive incidents on smallholders’ resilience. Resilience is indicated by farmers’ ability to adapt to changes, to recover from downturn business conditions or catastrophes, to anticipate risk, and to innovate new designs of farming activities. Resilience is categorized as less or more resilient (binary). The economic disruption is triggered by production, market, and investment circumstances. Meanwhile, ecological disruption is resulted from natural disasters, climate change, farmer’s treatment of the land, land fire, and government environmental policy. The result shows that more than 60% of smallholder oil palm plantations in Bengkulu Province are less resilient. Production uncertainty, bargaining position, climate change, and environmentally unfriendly farming behaviours increase the possibility of lowering smallholders’ resilience level.
Alcohol and the Brain

Alcohol works on the brain to produce its desired effects, e.g., sociability and intoxication, and hence the brain is an important organ for exploring subsequent harms. These come in many different forms such as the consequences of damage during intoxication, e.g., from falls and fights, damage from withdrawal, damage from the toxicity of alcohol and its metabolites and altered brain structure and function with implications for behavioral processes such as craving and addiction. On top of that are peripheral factors that compound brain damage such as poor diet, vitamin deficiencies leading to Wernicke-Korsakoff syndrome. Prenatal alcohol exposure can also have a profound impact on brain development and lead to irremediable changes of fetal alcohol syndrome. This chapter briefly reviews aspects of these with a particular focus on recent brain imaging results. Cardiovascular effects of alcohol that lead to brain pathology are not covered as they are dealt with elsewhere in the volume.
Mechanical Loading Modulates Gene Expression in Chondrocyte-Seeded Agarose Hydrogels

A successful tissue engineered articular cartilage construct needs to possess mechanical, biochemical, and histological features similar to that of native cartilage in order to serve its load-bearing function. Agarose is a suitable scaffold material for chondrocyte cultures (1,2), allowing long-term maintenance of cell phenotype and the elaboration of a functional cartilage-like matrix. This culture system facilitates further elucidation of the roles of matrix and cell-matrix interactions in the regulation of chondrocyte response to mechanical loads. We have previously shown (3) that mechanical loading at a physiologic frequency can increase the rate of matrix deposition, increasing mechanical properties of the tissue engineered constructs (∼21 fold increases in HA over day 0 with loading vs. ∼4 fold increases for free swelling controls). We have also shown that dynamic loading of transiently transfected chondrocytes in agarose hydrogels for 1 hour at 10% strain increased aggrecan promoter activity by ∼1.5 fold (4). In this study we sought to further characterize the short term response of chondrocytes to static load (by measuring aggrecan promoter activity) and the effects of dynamic compression on aggrecan gene expression over a longer (3 day) culture period (by monitoring mRNA levels). Monitoring matrix gene expression during early times of culture, when there is little matrix accumulation and the cells deform directly with the matrix (5), may provide insights into cellular responses to strain and allow for the optimization of cartilage bioreactor conditions.
A low power wide-band CMOS PLL frequency synthesizer for portable hybrid GNSS receiver

The design consideration and implementation of a CMOS frequency synthesizer for the portable hybrid global navigation satellite system are presented. The large tuning range is achieved by tuning curve compensation using an improved VCO resonant tank, which reduces the power consumption and obtains better phase noise performance. The circuit is validated by simulations and fabricated in a standard 0.18 μm 1P6M CMOS process. Close-loop phase noise measured is lower than −95 dBc at 200 kHz offset while the measured tuning range is 21.5% from 1.47 to 1.83 GHz. The proposed synthesizer including source coupled logic prescaler consumes 6.2 mA current from 1.8 V supply. The whole silicon required is only 0.53 mm2.
Simulation of far-field characteristics and measurement techniques for vehicle-mounted antennas

Numerical models of simple monopoles mounted on vehicles are presented which indicate that the far-field gain and radiation patterns for such systems can differ significantly from that of the ideal antenna. The theoretical results also suggest that very significant antenna separations (>30 m) may be required in order to carry out gain measurements using simple transmission measurements for vehicles located on a conducting ground plane. The measured coupling to a test antenna at 5 m range is comparable with simulations based on a TLM model of this arrangement. These results give some confidence in the validity of the estimated far-field characteristics, since the latter were derived from predicted fields in this region. (8 pages)
A Genetic Algorithm for Bus Schedule Synchronization

The bus transfers synchronization problem is to find an optimal bus schedule for the entire transit system that minimizes riders’ transfer time. This is a complicated problem of the large set of binary and discrete values involved. The combinatorial nature of the problem poses a computational burden and makes it difficult to solve using classical methods. This paper presents a Genetic Algorithm (GA) approach to synchronizing bus schedules to minimize transfer times. The algorithm takes existing scheduled timetables and ridership data at transfer locations as input and addresses the randomness of bus arrivals. The algorithm takes existing scheduled timetables and ridership data at transfer locations as input and addresses randomness in bus arrivals. The algorithm attempts to find an optimum solution for the bus schedule synchronization problem by shifting existing timetables. Using scheduling data from Broward County Transit, total passenger transfer times were calculated for the existing and the proposed systems. This algorithm was able to reduce system-wide transfer time by 13.4%. Results from this case study and recommendations for future research are presented.