Now showing items 1-20 of 52647

• #### Control of the CDC48A segregase by the plant UBX-containing (PUX) protein family

(2021-05) [Thesis]
Committee members: Blilou, Ikram; Jaremko, Lukasz
In plants, AAA-adenosine triphosphatase (ATPase) Cell Division Control Protein 48 (CDC48) uses the force generated through ATP hydrolysis to pull, extract, and unfold ubiquitylated or sumoylated proteins from the membrane, chromatin, or protein complexes. The resulting changes in protein or RNA content are an important means for plants to control protein homeostasis and thereby adapt to shifting environmental conditions. The activity and targeting of CDC48 are controlled by adaptor proteins, of which the plant ubiquitin regulatory X (UBX) domain-containing (PUX) proteins constitute the largest and most versatile family. However, few PUX proteins have been structurally or functionally characterized and how they participate in the substrate processing of CDC48A is not fully understood. Here, we first performed a comparative bioinformatic analysis, in which we found that the PUX proteins can be functionally divided into six types. We used this classification as a guide for our experimental efforts to elucidate how PUX proteins mediate client recognition and delivery for CDC48A-mediated unfolding. As a first step in this experimental analysis, we cloned and expressed a number of PUX protein constructs, we assessed their interaction features, and obtained crystals for several PUX domains. These bioinformatic and experimental results provide a basis for the in-depth structural and functional analysis of how PUX proteins control the CDC48A segregase.
• #### Controlling Electrochemically Induced Volume Changes in Conjugated Polymers by Chemical Design: from Theory to Devices

(Advanced Functional Materials, Wiley, 2021-04-17) [Article]
Electrochemically induced volume changes in organic mixed ionic-electronic conductors (OMIECs) are particularly important for their use in dynamic microfiltration systems, biomedical machinery, and electronic devices. Although significant advances have been made to maximize the dimensional changes that can be accomplished by OMIECs, there is currently limited understanding of how changes in their molecular structures impact their underpinning fundamental processes and their performance in electronic devices. Herein, a series of ethylene glycol functionalized conjugated polymers is synthesized, and their electromechanical properties are evaluated through a combined approach of experimental measurements and molecular dynamics simulations. As demonstrated, alterations in the molecular structure of OMIECs impact numerous processes occurring during their electrochemical swelling, with sidechain length shortening decreasing the number of incorporated water molecules, reducing the generated void volumes and promoting the OMIECs to undergo different phase transitions. Ultimately, the impact of these combined molecular processes is assessed in organic electrochemical transistors, revealing that careful balancing of these phenomena is required to maximize device performance.
• #### Augmented Reality in Medical Practice: From Spine Surgery to Remote Assistance.

(Frontiers in surgery, Frontiers Media SA, 2021-04-16) [Article]
Background: While performing surgeries in the OR, surgeons and assistants often need to access several information regarding surgical planning and/or procedures related to the surgery itself, or the accessory equipment to perform certain operations. The accessibility of this information often relies on the physical presence of technical and medical specialists in the OR, which is increasingly difficult due to the number of limitations imposed by the COVID emergency to avoid overcrowded environments or external personnel. Here, we analyze several scenarios where we equipped OR personnel with augmented reality (AR) glasses, allowing a remote specialist to guide OR operations through voice and $\textit{ad-hoc}$ visuals, superimposed to the field of view of the operator wearing them. Methods: This study is a preliminary case series of prospective collected data about the use of AR-assistance in spine surgery from January to July 2020. The technology has been used on a cohort of 12 patients affected by degenerative lumbar spine disease with lumbar sciatica co-morbidities. Surgeons and OR specialists were equipped with AR devices, customized with P2P videoconference commercial apps, or customized holographic apps. The devices were tested during surgeries for lumbar arthrodesis in a multicenter experience involving author's Institutions. Findings: A total number of 12 lumbar arthrodesis have been performed while using the described AR technology, with application spanning from telementoring (3), teaching (2), surgical planning superimposition and interaction with the hologram using a custom application for Microsoft hololens (1). Surgeons wearing the AR goggles reported a positive feedback as for the ergonomy, wearability and comfort during the procedure; being able to visualize a 3D reconstruction during surgery was perceived as a straightforward benefit, allowing to speed-up procedures, thus limiting post-operational complications. The possibility of remotely interacting with a specialist on the glasses was a potent added value during COVID emergency, due to limited access of non-resident personnel in the OR. Interpretation: By allowing surgeons to overlay digital medical content on actual surroundings, augmented reality surgery can be exploited easily in multiple scenarios by adapting commercially available or custom-made apps to several use cases. The possibility to observe directly the operatory theater through the eyes of the surgeon might be a game-changer, giving the chance to unexperienced surgeons to be virtually at the site of the operation, or allowing a remote experienced operator to guide wisely the unexperienced surgeon during a procedure.
• #### Antennal transcriptome sequencing and identification of candidate chemoreceptor proteins from an invasive pest, the American palm weevil, Rhynchophorus palmarum.

(Scientific reports, Springer Science and Business Media LLC, 2021-04-16) [Article]
For decades, the American palm weevil (APW), Rhynchophorus palmarum, has been a threat to coconut and oil palm production in the Americas. It has recently spread towards North America, endangering ornamental palms, and the expanding date palm production. Its behavior presents several parallelisms with a closely related species, R. ferrugineus, the red palm weevil (RPW), which is the biggest threat to palms in Asia and Europe. For both species, semiochemicals have been used for management. However, their control is far from complete. We generated an adult antennal transcriptome from APW and annotated chemosensory related gene families to obtain a better understanding of these species' olfaction mechanism. We identified unigenes encoding 37 odorant-binding proteins (OBPs), ten chemosensory proteins (CSPs), four sensory neuron membrane proteins (SNMPs), seven gustatory receptors (GRs), 63 odorant receptors (ORs), and 28 ionotropic receptors (IRs). Noticeably, we find out the R. ferrugineus pheromone-binding protein and pheromone receptor orthologs from R. palmarum. Candidate genes identified and annotated in this study allow us to compare these palm weevils' chemosensory gene sets. Most importantly, this study provides the foundation for functional studies that could materialize as novel pest management strategies.
• #### Reimagining aquaculture in the Global South.

(Science (New York, N.Y.), American Association for the Advancement of Science (AAAS), 2021-04-16) [Article]
Aquaculture has existed for millennia, reaching industrial scales in recent decades, and will play an increasingly important role in feeding the world (1–6). As this industry grows, we must ensure that it is ecologically and socially sustainable. However, the current production process for the food given to farmed fish still threatens coastal ecosystems and the livelihoods of local fishers, especially in the Global South (2–7). Before aquaculture is scaled up further, its global environmental and socioeconomic footprint should be carefully reimagined.
• #### Modulation of electronic and magnetic properties of monolayer chromium trihalides by alloy and strain engineering

(Journal of Applied Physics, AIP Publishing, 2021-04-16) [Article]
Monolayer CrI3 is a rare ferromagnetic semiconductor with intrinsic long-range magnetic order, which makes it a great potential material in spintronic devices [Song et al., Science 360, 1214 (2018)]. To extend the applications of monolayer CrI3 in flexible devices, the modulation of its electronic and magnetic properties is important. Here, we investigated the combined effect of strain and alloy on the properties of monolayer CrI3 by first-principles calculations. Br is chosen as the alloyed element due to the similar atomic configuration and property of CrX3 (X = Br, I), and the strain is applied by simultaneously changing the in-plane lattice constants (a and b). We find that the bandgap of monolayer Cr2I6−xBrx can be tuned greatly, while the magnetic moment of monolayer Cr2I6−xBrx is regulated very little under different strain and Br concentration. This unique property of monolayer Cr2I6−xBrx under strain makes it a good candidate for the flexible spintronic devices.
• #### Skyrmion battery effect via inhomogeneous magnetic anisotropy

(Applied Physics Reviews, AIP Publishing, 2021-04-14) [Article]
Magnetic skyrmions are considered a promising candidate for the next-generation information processing technology. Being topologically robust, magnetic skyrmions are swirling spin textures that can be used in a broad range of applications from memory devices and logic circuits to neuromorphic computing. In a magnetic medium lacking inversion symmetry, magnetic skyrmion arises as a result of the interplay among magnetic exchange interaction, Dzyaloshinskii-Moriya interaction, and magnetic anisotropy. Instrumental to the integrated skyrmion-based applications are the creation and manipulation of magnetic skyrmions at a designated location, absent any need of a magnetic field. In this paper, we propose a generic design strategy to achieve that goal and a model system to demonstrate its feasibility. By implementing a disk-shaped thin film heterostructure with an inhomogeneous perpendicular magnetic anisotropy, stable sub-100-nm size skyrmions can be generated without magnetic field. This structure can be etched out via, for example, focused ion beam microscope. Using micromagnetic simulation, we show that such heterostructure not only stabilizes the edge spins of the skyrmion but also protects its rotation symmetry. Furthermore, we may switch the spin texture between skyrmionic and vortex-like ones by tuning the slope of perpendicular anisotropy using a bias voltage. When embedded into a magnetic conductor and under a spin polarized current, such heterostructure emits skyrmions continuously and may function as a skyrmion source. This unique phenomenon is dubbed a skyrmion battery effect. Our proposal may open a novel venue for the realization of all-electric skyrmion-based devices.
• #### ENSO feedback drives variations in dieback at a marginal mangrove site

(Scientific Reports, Springer Science and Business Media LLC, 2021-04-14) [Article]
AbstractOcean–atmosphere climatic interactions, such as those resulting from El Niño Southern Oscillation (ENSO) are known to influence sea level, sea surface temperature, air temperature, and rainfall in the western Pacific region, through to the north-west Australian Ningaloo coast. Mangroves are ecologically important refuges for biodiversity and a rich store of blue carbon. Locations such as the study site (Mangrove Bay, a World Heritage Site within Ningaloo Marine Park and Cape Range National Park) are at the aridity range-limit which means trees are small in stature, forests small in area, and are potentially susceptible to climate variability such as ENSO that brings lower sea level and higher temperature. Here we explore the relationship between mangrove dieback, and canopy condition with climatic variables and the Southern Oscillation Index (SOI)—a measure of ENSO intensity, through remote sensing classification of Landsat satellite missions across a 29 year period at a north-west Australian site. We find that the SOI, and seasonal mean minimum temperature are strongly correlated to mangrove green canopy (as indicator of live canopy) area. This understanding of climate variations and mangrove temporal heterogeneity (patterns of abundance and condition) highlights the sensitivity and dynamics of this mangrove forest and recommends further research in other arid and semi-arid tropical regions at mangrove range-limits to ascertain the extent of this relationship.
• #### Toward Improving the Internet of Things: Quality of Service and Fault Tolerance Perspectives

(2021-04-13) [Dissertation]
Committee members: Alouini, Mohamed-Slim; Zhang, Xiangliang; Bessani, Alysson
The Internet of Things (IoT) is a technology aimed at developing a global network of machines and devices that can interact and communicate with each other. Supporting IoT, therefore, requires revisiting the Internet's best e ort service model and reviewing its complex communication patterns. In this dissertation, we explore the unique characteristics of IoT tra c and examine IoT systems. Our work is motivated by the new capabilities o ered by modern Software De ned Networks (SDN) and blockchain technology. We evaluate IoT Quality of Service (QoS) in traditional networking. We obtain mathematical expressions to calculate end-to-end delay, and dropping. Our results provide insight into the advantages of an intelligent edge serving as a detection mechanism. Subsequently, we propose SADIQ, SDN-based Application-aware Dynamic Internet of things QoS. SADIQ provides context-driven QoS for IoT applications by allowing applications to express their requirements using a high-level SQL-like policy language. Our results show that SADIQ improves the percentage of regions with an error in their reported temperature for the Weather Signal application up to 45 times; and it improves the percentage of incorrect parking statuses for regions with high occupancy for the Smart Parking application up to 30 times under the same network conditions and drop rates. Despite centralization and the control of data, IoT systems are not safe from cyber-crime, privacy issues, and security breaches. Therefore, we explore blockchain technology. In the context of IoT, Byzantine fault tolerance-based consensus protocols are used. However, the blockchain consensus layer contributes to the most remarkable performance overhead especially for IoT applications subject to maximum delay constraints. In order to capture the unique requirements of the IoT, consensus mechanisms and block formation need to be redesigned. To this end, we propose Synopsis, a novel hierarchical blockchain system. Synopsis introduces a wireless-optimized Byzantine chain replication protocol and a new probabilistic data structure. The results show that Synopsis successfully reduces the memory footprint from Megabytes to a few Kilobytes with an improvement of 1000 times. Synopsis also enables reductions in message complexity and commitment delay of 85% and 99.4%, respectively.
• #### Significant variants of type 2 diabetes in the Arabian Region through an Integration of exome databases.

(PloS one, Public Library of Science (PLoS), 2021-04-13) [Article]
Type 2 diabetes (T2D) is a major global health issue, and it has also become one of the major diseases in Arab countries. In addition to the exome databases that have already been established, whole exome sequencing data for the Greater Middle East are now available. To elucidate the genetic features of T2D in the Arabian Peninsula, we integrated two exome databases (gnomAD exome and the Greater Middle East Variome Project) with clinical information from the ClinVar. After the integration, we obtained 18 single nucleotide polymorphisms and found two statistically and clinically significant variants in two genes, SLC30A8 rs13266634 and KCNJ11 rs5219. Interestingly, the two genes are linked to the uptake of the metals, Zn and K respectively, which indicating the regional features of the genetic variants. The frequency of the risk allele of rs13266634 among individuals in the Arabian Peninsula was higher than among individuals in other regions. On the other hand, the frequency of the risk allele of rs5219 in the Arabian Peninsula was lower than that in other regions. We identified and characterized T2D-related variants that show unique tendencies in the Arabian Peninsula. Our analyses contribute to and provide guidance for the clinical research of T2D in the Arabian Peninsula.
• #### Can a recipe for the growth of single-layer graphene on copper be used in different chemical vapor deposition reactors?

(Chemistry, an Asian journal, Wiley, 2021-04-13) [Article]
In the last decade, catalytic chemical vapor deposition (CVD) has been intensively explored for the growth of single-layer graphene (SLG). Despite the scattering of guidelines and procedures, variables such as the surface texture/chemistry of catalyst metal foils, carbon feedstock, and growth process parameters have been well-scrutinized. Still, questions remain on how best to standardize the growth procedure. The possible correlation of recipes between different CVD setups is an example. Here, two thermal CVD reactors were explored to grow graphene on Cu foil. The design of these setups was entirely distinct, one being a "showerhead" cold-wall type, whereas the other represented the popular "tubular" hot-wall type. Upon standardizing the Cu foil surface, it was possible to develop a recipe for cm 2 -scale SLG growth that differed only on the carrier gas flow rate used in the two reactors.
• #### Improved characterisation of clinical text through ontology-based vocabulary expansion.

(Journal of biomedical semantics, Springer Science and Business Media LLC, 2021-04-13) [Article]
BackgroundBiomedical ontologies contain a wealth of metadata that constitutes a fundamental infrastructural resource for text mining. For several reasons, redundancies exist in the ontology ecosystem, which lead to the same entities being described by several concepts in the same or similar contexts across several ontologies. While these concepts describe the same entities, they contain different sets of complementary metadata. Linking these definitions to make use of their combined metadata could lead to improved performance in ontology-based information retrieval, extraction, and analysis tasks.ResultsWe develop and present an algorithm that expands the set of labels associated with an ontology class using a combination of strict lexical matching and cross-ontology reasoner-enabled equivalency queries. Across all disease terms in the Disease Ontology, the approach found 51,362 additional labels, more than tripling the number defined by the ontology itself. Manual validation by a clinical expert on a random sampling of expanded synonyms over the Human Phenotype Ontology yielded a precision of 0.912. Furthermore, we found that annotating patient visits in MIMIC-III with an extended set of Disease Ontology labels led to semantic similarity score derived from those labels being a significantly better predictor of matching first diagnosis, with a mean average precision of 0.88 for the unexpanded set of annotations, and 0.913 for the expanded set.ConclusionsInter-ontology synonym expansion can lead to a vast increase in the scale of vocabulary available for text mining applications. While the accuracy of the extended vocabulary is not perfect, it nevertheless led to a significantly improved ontology-based characterisation of patients from text in one setting. Furthermore, where run-on error is not acceptable, the technique can be used to provide candidate synonyms which can be checked by a domain expert.
• #### Big Communications: Connect the Unconnected

(arXiv, 2021-04-13) [Preprint]
In this article, we present the analysis of the digital divide to illustrate the unfair access to the benefits brought by information and communications technology (ICT) over the globe and provide our solution termed big communications (BigCom) to close the digital divide and democratize the benefits of ICT. To facilitate the implementation of BigCom, we give a complete framework of BigCom considering both technological and non-technological factors as well as a set of suggestions for content providers, mobile network operators, and governments. By implementing BigCom, we aim to connect the last four billion unconnected people living in far-flung and underdeveloped areas and achieve the goal of global and ubiquitous connectivity for everyone in the 6G era.
• #### The presence of Superfund sites as a determinant of life expectancy in the United States

(Nature Communications, Springer Science and Business Media LLC, 2021-04-13) [Article]
AbstractSuperfund sites could affect life expectancy (LE) via increasing the likelihood of exposure to toxic chemicals. Here, we assess to what extent such presence could alter the LE independently and in the context of sociodemographic determinants. A nationwide geocoded statistical modeling at the census tract level was undertaken to estimate the magnitude of impact. Results showed a significant difference in LE among census tracts with at least one Superfund site and their neighboring tracts with no sites. The presence of a Superfund site could cause a decrease of −0.186 ± 0.027 years in LE. This adverse effect could be as high as −1.22 years in tracts with Superfund sites and high sociodemographic disadvantage. Specific characteristics of Superfund sites such as being prone to flooding and the absence of a cleanup strategy could amplify the adverse effect. Furthermore, the presence of Superfund sites amplifies the negative influence of sociodemographic factors at lower LEs.
• #### Wide-field-of-view optical detectors using fused fiber-optic tapers

(Optics Letters, The Optical Society, 2021-04-12) [Article]
Photodetectors used in wireless applications suffer from a trade-off between their response speeds and their active areas, which limits the received signal-to-noise ratio (SNR). Conventional light-focusing elements used to improve the SNR narrow the field of view (FOV). Herein, we demonstrate a versatile imaging light-focusing element featuring a wide FOV and high optical gain using fused fiber-optic tapers. To verify the practicality of the proposed design, we demonstrated and tested a wide-FOV optical detector for optical wireless communication that can be used for wavelengths ranging from the visible-light band to the near infrared. The proposed detector offers improvements over luminescent wide-FOV detectors, including higher efficiency, a broader modulation bandwidth, and indefinite stability.
• #### Snapshot space-time holographic three-dimensional particle tracking velocimetry

(Laser & Photonics Reviews, Wiley-VCH, 2021-04-12) [Article]
Digital inline holography is an amazingly simple and effective approach for three-dimensional imaging, to which particle tracking velocimetry is of particular interest. Conventional digital holographic particle tracking velocimetry techniques are computationally separated in particle and flow reconstruction, plus the expensive computations. Usually, the particle volumes are recovered firstly, from which fluid flows are computed. Without iterative reconstructions, This sequential spacetime process lacks accuracy. This paper presents a joint optimization framework for digital holographic particle tracking velocimetry: particle volumes and fluid flows are reconstructed jointly in a higher space-time dimension, enabling faster convergence and better reconstruction quality of both fluid flow and particle volumes within a few minutes on modern GPUs. Synthetic and experimental results are presented to show the efficiency of the proposed technique.
• #### Seagrass (Halophila stipulacea) invasion enhances carbon sequestration in the Mediterranean Sea.

(Global change biology, Wiley, 2021-04-12) [Article]
The introduction and establishment of exotic species often result in significant changes in recipient communities and their associated ecosystem services. However, usually the magnitude and direction of the changes are difficult to quantify because there is no pre-introduction data. Specifically, little is known about the effect of marine exotic macrophytes on organic carbon sequestration and storage. Here, we combine dating sediment cores (210Pb) with sediment eDNA fingerprinting to reconstruct the chronology of pre- and post-arrival of the Red Sea seagrass Halophila stipulacea spreading into the Eastern Mediterranean native seagrass meadows. We then compare sediment organic carbon storage and burial rates before and after the arrival of H. stipulacea and between exotic (H. stipulacea) and native (C. nodosa and P. oceanica) meadows since the time of arrival following a Before-After-Control-Impact (BACI) approach. This analysis revealed that H. stipulacea arrived at the areas of study in Limassol (Cyprus) and West Crete (Greece) in the 1930s and 1970s, respectively. Average sediment organic carbon after the arrival of H. stipulacea to the sites increased in the exotic meadows twofold, from 8.4 ± 2.5 g Corg m−2 year−1 to 14.7 ± 3.6 g Corg m−2 year−1, and, since then, burial rates in the exotic seagrass meadows were higher than in native ones of Cymodocea nodosa and Posidonia oceanica. Carbon isotopic data indicated a 50% increase of the seagrass contribution to the total sediment Corg pool since the arrival of H. stipulacea. Our results demonstrate that the invasion of H. stipulacea may play an important role in maintaining the blue carbon sink capacity in the future warmer Mediterranean Sea, by developing new carbon sinks in bare sediments and colonizing areas previously occupied by the colder thermal affinity P. oceanica.
• #### Investigation of InGaN-based red/green micro-light-emitting diodes

(Optics Letters, The Optical Society, 2021-04-12) [Article]
We investigated the performance of InGaN-based red/green micro-light-emitting diodes (µLEDs) ranging from 98 × 98 µm2 to 17 × 17 µm. The average forward voltage at 10 A/cm2 was independent of the dimension of µLEDs. Red µLEDs exhibited a larger blueshift of the peak wavelength (∼35 nm) and broader full-width at half maximum (≥50 nm) at 2−50 A/cm2 compared to green µLEDs. We demonstrated that 47 × 47 µm2 red µLEDs had an on-wafer external quantum efficiency of 0.36% at the peak wavelength of 626 nm, close to the red primary color defined in the recommendation 2020 standard.
• #### Nonlinear valley phonon scattering under the strong coupling regime

(Nature Materials, Springer Science and Business Media LLC, 2021-04-12) [Article]
Research efforts of cavity quantum electrodynamics have focused on the manipulation of matter hybridized with photons under the strong coupling regime1,2,3. This has led to striking discoveries including polariton condensation2 and single-photon nonlinearity3, where the phonon scattering plays a critical role1,2,3,4,5,6,7,8,9. However, resolving the phonon scattering remains challenging for its non-radiative complexity. Here we demonstrate nonlinear phonon scattering in monolayer MoS2 that is strongly coupled to a plasmonic cavity mode. By hybridizing excitons and cavity photons, the phonon scattering is equipped with valley degree of freedom and boosted with superlinear enhancement to a stimulated regime, as revealed by Raman spectroscopy and our theoretical model. The valley polarization is drastically enhanced and sustained throughout the stimulated regime, suggesting a coherent scattering process enabled by the strong coupling. Our findings clarify the feasibility of valley–cavity-based systems for lighting, imaging, optical information processing and manipulating quantum correlations in cavity quantum electrodynamics2,3,10,11,12,13,14,15,16,17.