Now showing items 1-20 of 48433

• #### High rates of carbon and dinitrogen fixation suggest a critical role of benthic pioneer communities in the energy and nutrient dynamics of coral reefs

(Functional Ecology, Wiley, 2020-07-02) [Article]
1. Following coral mortality in tropical reefs, pioneer communities dominated by filamentous and crustose algae efficiently colonize substrates previously occupied by coral tissue. This phenomenon is particularly common after mass coral mortality following prolonged bleaching events associated with marine heatwaves. 2. Pioneer communities play an important role for the biological succession and reorganization of reefs after disturbance. However, their significance for critical ecosystem functions previously mediated by corals, such as the efficient cycling of carbon (C) and nitrogen (N) within the reef, remains uncertain. 3. We used 96 carbonate tiles to simulate the occurrence of bare substrates after disturbance in a coral reef of the central Red Sea. We measured rates of C and dinitrogen (N2) fixation of pioneer communities on these tiles monthly over an entire year. Coupled with elemental and stable isotope analyses, these measurements provide insights into macronutrient acquisition, export, and the influence of seasonality. 4. Pioneer communities exhibited high rates of C and N2 fixation within 4 – 8 weeks after the introduction of experimental bare substrates. Ranging from 13 to 25 μmol C cm−2 d−1 and 8 to 54 nmol N cm−2 d−1, respectively, C and N2 fixation rates were comparable to reported values for established Red Sea coral reefs. This similarity indicates that pioneer communities may quickly compensate for the loss of benthic productivity by corals. Notably, between 40 and 85% of fixed organic C was exported into the environment, constituting a vital source of energy for the coral reef food web. 5. Our findings suggest that benthic pioneer communities may play a crucial, yet overlooked role in the C and N dynamics of oligotrophic coral reefs by contributing to the input of new C and N after coral mortality. While not substituting other critical ecosystem functions provided by corals (e.g. structural habitat complexity and coastal protection), pioneer communities likely contribute to maintaining coral reef nutrient cycling through the accumulation of biomass and import of macronutrients following coral loss.
• #### Early-Stage Growth Mechanism and Synthesis Conditions-Dependent Morphology of Nanocrystalline Bi Films Electrodeposited from Perchlorate Electrolyte.

(Nanomaterials (Basel, Switzerland), MDPI AG, 2020-07-02) [Article]
Bi nanocrystalline films were formed from perchlorate electrolyte (PE) on Cu substrate via electrochemical deposition with different duration and current densities. The microstructural, morphological properties, and elemental composition were studied using scanning electron microscopy (SEM), atomic force microscopy (AFM), and energy-dispersive X-ray microanalysis (EDX). The optimal range of current densities for Bi electrodeposition in PE using polarization measurements was demonstrated. For the first time, it was shown and explained why, with a deposition duration of 1 s, co-deposition of Pb and Bi occurs. The correlation between synthesis conditions and chemical composition and microstructure for Bi films was discussed. The analysis of the microstructure evolution revealed the changing mechanism of the films' growth from pillar-like (for Pb-rich phase) to layered granular form (for Bi) with deposition duration rising. This abnormal behavior is explained by the appearance of a strong Bi growth texture and coalescence effects. The investigations of porosity showed that Bi films have a closely-packed microstructure. The main stages and the growth mechanism of Bi films in the galvanostatic regime in PE with a deposition duration of 1-30 s are proposed.
• #### Alternative splicing and allosteric regulation modulate the chromatin binding of UHRF1.

(Nucleic acids research, Oxford University Press (OUP), 2020-07-02) [Article]
UHRF1 is an important epigenetic regulator associated with apoptosis and tumour development. It is a multidomain protein that integrates readout of different histone modification states and DNA methylation with enzymatic histone ubiquitylation activity. Emerging evidence indicates that the chromatin-binding and enzymatic modules of UHRF1 do not act in isolation but interplay in a coordinated and regulated manner. Here, we compared two splicing variants (V1, V2) of murine UHRF1 (mUHRF1) with human UHRF1 (hUHRF1). We show that insertion of nine amino acids in a linker region connecting the different TTD and PHD histone modification-binding domains causes distinct H3K9me3-binding behaviour of mUHRF1 V1. Structural analysis suggests that in mUHRF1 V1, in contrast to V2 and hUHRF1, the linker is anchored in a surface groove of the TTD domain, resulting in creation of a coupled TTD-PHD module. This establishes multivalent, synergistic H3-tail binding causing distinct cellular localization and enhanced H3K9me3-nucleosome ubiquitylation activity. In contrast to hUHRF1, H3K9me3-binding of the murine proteins is not allosterically regulated by phosphatidylinositol 5-phosphate that interacts with a separate less-conserved polybasic linker region of the protein. Our results highlight the importance of flexible linkers in regulating multidomain chromatin binding proteins and point to divergent evolution of their regulation.
• #### DTiGEMS+: drug–target interaction prediction using graph embedding, graph mining, and similarity-based techniques.

(Journal of Cheminformatics, Springer Science and Business Media LLC, 2020-07-02) [Article]
In silico prediction of drug–target interactions is a critical phase in the sustainable drug development process, especially when the research focus is to capitalize on the repositioning of existing drugs. However, developing such computational methods is not an easy task, but is much needed, as current methods that predict potential drug–target interactions suffer from high false-positive rates. Here we introduce DTiGEMS+, a computational method that predicts Drug–Target interactions using Graph Embedding, graph Mining, and Similarity-based techniques. DTiGEMS+ combines similarity-based as well as feature-based approaches, and models the identification of novel drug–target interactions as a link prediction problem in a heterogeneous network. DTiGEMS+ constructs the heterogeneous network by augmenting the known drug–target interactions graph with two other complementary graphs namely: drug–drug similarity, target–target similarity. DTiGEMS+ combines different computational techniques to provide the final drug target prediction, these techniques include graph embeddings, graph mining, and machine learning. DTiGEMS+ integrates multiple drug–drug similarities and target–target similarities into the final heterogeneous graph construction after applying a similarity selection procedure as well as a similarity fusion algorithm. Using four benchmark datasets, we show DTiGEMS+ substantially improves prediction performance compared to other state-of-the-art in silico methods developed to predict of drug-target interactions by achieving the highest average AUPR across all datasets (0.92), which reduces the error rate by 33.3% relative to the second-best performing model in the state-of-the-art methods comparison.
• #### Principal symmetric meshes

(ACM Transactions on Graphics, ACM, 2020-07) [Article]
The isolines of principal symmetric surface parametrizations run symmetrically to the principal directions. We describe two discrete versions of these special nets/quad meshes which are dual to each other and show their usefulness for various applications in the context of fabrication and architectural design. Our discretization of a principal symmetric mesh comes naturally with a family of spheres, the so-called Meusnier and Mannheim spheres. In our representation of principal symmetric meshes, we have direct control over the radii of theses spheres and the intersection angles of the parameter lines. This facilitates tasks such as generating Weingarten surfaces including constant mean curvature surfaces and minimal surfaces. We illustrate the potential of Weingarten surfaces for paneling doubly curved freeform facades by significantly reducing the number of necessary molds. Moreover, we have direct access to curvature adaptive tool paths for cylindrical CNC milling with circular edges as well as flank milling with rotational cones. Furthermore, the construction of curved support structures from congruent circular strips is easily managed by constant sphere radii. The underlying families of spheres are in a natural way discrete curvature spheres in analogy to smooth Möbius and Laguerre geometry which further leads to a novel discrete curvature theory for principal symmetric meshes.
• #### Rate-dependent viscoelasticity of an impact-hardening polymer under oscillatory shear

(Materials Research Express, IOP Publishing, 2020-07-01) [Article]
The rate-dependent effect of viscoelasticity plays a critical role in the hardening mechanisms of impact-hardening polymers (IHP) when forcefully impacted. In this study, we used dynamic mechanical analysis (DMA) to characterize the rate-dependent viscoelasticity of an IHP under oscillatory shear. We found that the storage modulus increased by three orders of magnitude within the experimental range when the oscillatory frequency varied from 0.1 to 100 rad/s. To further understand the real strain rate effect of IHP, we introduced the Havriliak-Negami (H–N) model to predict the dynamic viscoelastic behaviors of the IHP for a wider frequency range (from zero to infinity) than that applied in the DMA experiments. Based on the H–N model results, we defined a parameter to describe the rate-dependent effect of the IHP, which was not dependent on the frequency range and reflected the intrinsic material properties of IHP. We used the time-temperature superposition principle (TTSP), which extended the experimental range from 0.1 rad s−1 down to 0.005 rad s−1, to verify the accuracy of the rate-dependent viscoelasticity predicted by the H–N model. Finally, we outlined the influence of temperature on the dynamic viscoelastic behaviors of IHP and discussed the phase transition mechanism induced by temperature and the oscillatory frequency. The results presented here not only provide a method (i.e., by combining experimental results with the H–N model results) to characterize the real rate-dependent viscoelasticity of IHP but are also valuable to further our understanding of the impact-hardening mechanisms of IHP.
• #### Bulk Spin Torque-Driven Perpendicular Magnetization Switching in L10 FePt Single Layer.

(Advanced materials (Deerfield Beach, Fla.), Wiley, 2020-06-30) [Article]
Due to its inherent superior perpendicular magnetocrystalline anisotropy, the FePt in L10 phase enables magnetic storage and memory devices with ultrahigh capacity. However, reversing the FePt magnetic state, and therefore encoding information, has proven to be extremely difficult. Here, it is demonstrated that an electric current can exert a large spin torque on an L10 FePt magnet, ultimately leading to reversible magnetization switching. The spin torque monotonically increases with increasing FePt thickness, exhibiting a bulk characteristic. Meanwhile, the spin torque effective fields and switching efficiency increase as the FePt approaches higher chemical ordering with stronger spin-orbit coupling. The symmetry breaking that generates spin torque within L10 FePt is shown to arise from an inherent structural gradient along the film normal direction. By artificially reversing the structural gradient, an opposite spin torque effect in L10 FePt is demonstrated. At last, the role of the disorder gradient in generating a substantial torque in a single ferromagnet is supported by theoretical calculations. These results will push forward the frontier of material systems for generating spin torques and will have a transformative impact on magnetic storage and spin memory devices with simple architecture, ultrahigh density, and readily application.
• #### Functional pangenome analysis points to protein E, a pathogenicity determinant in SARS, as a therapeutic target for COVID-19 complications

(Frontiers in Cellular and Infection Microbiology, Frontiers, 2020-06-30) [Article]
The spread of the novel coronavirus (SARS-CoV-2) has triggered a global emergency, that demands urgent solutions for detection and therapy to prevent escalating health, social and economic impacts. The spike protein (S) of this virus enables binding to the human receptor ACE2, and hence presents a prime target for vaccines preventing viral entry into host cells. The S proteins from SARS and SARS-CoV-2 are similar, but structural differences in the receptor binding domain (RBD) preclude the use of SARS-specific neutralizing antibodies to inhibit SARS-CoV-2. Here we used comparative pangenomic analysis of all sequenced reference Betacoronaviruses, complemented with functional and structural analyses. This analysis reveals that, among all core gene clusters present in these viruses, the envelope protein E shows a variant cluster shared by SARS and SARS-Cov2 with two completely-conserved key functional features, namely an ion-channel and a PDZ-binding motif (PBM). These features play a key role in the activation of the inflammasome causing the acute respiratory distress syndrome, the leading cause of death in SARS and SARS-CoV-2 infections. Together with functional pangenomic analysis, mutation tracking and previous evidence, on E protein as a determinant of pathogenicity in SARS, we suggest E protein as a therapeutic target for further studies to reduce complications of SARS-CoV-2 infections in COVID-19.
• #### Evidence for Silica Surface Three- and Five-Membered Metallacycle Intermediates in the Catalytic Cycle of Hydroaminoalkylation of Olefins Using Single-Ti-Metal Catalysts

(Organometallics, American Chemical Society (ACS), 2020-06-30) [Article]
The single-site silica-supported group IV metal amido complex [Ti(NMe2)4] gives the tris(amido)-supported fragment [(=Si−O−)Ti(−NMe2)3], which transforms into a three-membered metallacycle (called a metallaaziridine) by an αH transfer between two amido ligands. When the three-membered metallacycle reacts with 1-octene, it gives a five-membered metallacycle by insertion of the double bond into the M−C bond of the metallaziridine. These two metallacycles, key intermediates in the catalytic cycle of the hydroaminoalkylation of terminal olefins, were isolated and fully characterized following the surface organometallic chemistry (SOMC) concept and procedures. This paper shows that surface organometallic chemistry can be used to identify and fully characterize three- and five-membered metallacycles of Ti in the hydroaminoalkylation of olefins.
• #### Efficient Acceleration of Stencil Applications through In-Memory Computing

(Micromachines, MDPI AG, 2020-06-29) [Article]
<jats:p>The traditional computer architectures severely suffer from the bottleneck between the processing elements and memory that is the biggest barrier in front of their scalability. Nevertheless, the amount of data that applications need to process is increasing rapidly, especially after the era of big data and artificial intelligence. This fact forces new constraints in computer architecture design towards more data-centric principles. Therefore, new paradigms such as in-memory and near-memory processors have begun to emerge to counteract the memory bottleneck by bringing memory closer to computation or integrating them. Associative processors are a promising candidate for in-memory computation, which combines the processor and memory in the same location to alleviate the memory bottleneck. One of the applications that need iterative processing of a huge amount of data is stencil codes. Considering this feature, associative processors can provide a paramount advantage for stencil codes. For demonstration, two in-memory associative processor architectures for 2D stencil codes are proposed, implemented by both emerging memristor and traditional SRAM technologies. The proposed architecture achieves a promising efficiency for a variety of stencil applications and thus proves its applicability for scientific stencil computing.</jats:p>
• #### Photonics based perfect secrecy cryptography: Toward fully classical implementations

(Applied Physics Letters, AIP Publishing, 2020-06-29) [Article]
Developing an unbreakable cryptography is a long-standing question and a global challenge in the internet era. Photonics technologies are at the frontline of research, aiming at providing the ultimate system with capability to end the cybercrime industry by changing the way information is treated and protected now and in the long run. Such a perspective discusses some of the current challenges as well as opportunities that classical and quantum systems open in the field of cryptography as both a field of science and engineering.
• #### All-Polycarbonate Thermoplastic Elastomers Based on Triblock Copolymers Derived from Triethylborane-Mediated Sequential Copolymerization of CO2 with Various Epoxides

(Macromolecules, American Chemical Society (ACS), 2020-06-29) [Article]
Various oxirane monomers including alkyl ether or allyl-substituted ones such as 1-butene oxide, 1-hexene oxide, 1-octene oxide, butyl glycidyl ether, allyl glycidyl ether, and 2-ethylhexyl glycidyl ether were anionically copolymerized with CO2 into polycarbonates using onium salts as initiator in the presence of triethylborane. All copolymerizations exhibited a “living” character, and the monomer consumption was monitored by in situ Fourier-transform infrared spectroscopy. The various polycarbonate samples obtained were characterized by 1H NMR, GPC, and differential scanning calorimetry. In a second step, all-polycarbonate triblock copolymers demonstrating elastomeric behavior were obtained in one pot by sequential copolymerization of CO2 with two different epoxides, using a difunctional initiator. 1-Octene oxide was first copolymerized with CO2 to form the central soft poly(octene carbonate) block which was flanked by two external rigid poly(cyclohexene carbonate) blocks obtained through subsequent copolymerization of cyclohexene oxide with CO2. Upon varying the ratio of 1-octene oxide to cyclohexene oxide and their respective ratios to the initiator, three all-polycarbonate triblock samples were prepared with molar masses of about 350 kg/mol and 22, 26, and 29 mol % hard block content, respectively. The resulting triblock copolymers were analyzed using 1H NMR, GPC, thermogravimetric analysis, differential scanning calorimetry, and atomic force microscopy. All three samples demonstrated typical elastomeric behavior characterized by a high elongation at break and ultimate tensile strength in the same range as those of other natural and synthetic rubbers, in particular those used in applications such as tissue engineering.
• #### An in-field integrated capacitive sensor for rapid detection and quantification of soil moisture

(Sensors and Actuators B: Chemical, Elsevier BV, 2020-06-29) [Article]
The development of in-situ soil moisture sensors (SMS) with advanced materials is the requirement of the future autonomous agriculture industry. However, an open challenge for these sensors is to control changes in the capacitance rather than resistance while attaining reliability, high performance, scalability and stability. In this work, a series of materials such as Graphite oxide (GO), Molybdenum disulfide (MoS2), Vanadium oxide (V2O5), and Molybdenum oxide (MoO3) are tested in realizing a receptor layer that can efficiently sense soil moisture. Here, we found that MoS2 offers the sensitivity, which is nearly three times higher (1200 pF) than in the case of V2O5 for any given range of soil-moisture content outperforming both GO and MoO3 materials. The corresponding increase in the sensitivities for MoO3, GO, MoS2, and V2O5 are ∼13%, ∼11%, ∼30%, and ∼9% respectively, for a variety of temperature up to 45 °C. A temperature variation of 25 °C to 50 °C showed a minimal increase in the sensitivity response for all the devices. We further demonstrated a record sensitivity of 540% with MoS2 in black soil and the corresponding response time was 65 sec. Finally, the recovery time for the MoS2 sensor is 27 s, which is quite fast.
• #### QCL-Based Dual-Comb Spectrometer for Multi-Species Measurements at High Temperatures and High Pressures

(Sensors, MDPI AG, 2020-06-29) [Article]
<jats:p>Rapid multi-species sensing is an overarching goal in time-resolved studies of chemical kinetics. Most current laser sources cannot achieve this goal due to their narrow spectral coverage and/or slow wavelength scanning. In this work, a novel mid-IR dual-comb spectrometer is utilized for chemical kinetic investigations. The spectrometer is based on two quantum cascade laser frequency combs and provides rapid (4 µs) measurements over a wide spectral range (~1175–1235 cm−1). Here, the spectrometer was applied to make time-resolved absorption measurements of methane, acetone, propene, and propyne at high temperatures (>1000 K) and high pressures (>5 bar) in a shock tube. Such a spectrometer will be of high value in chemical kinetic studies of future fuels.</jats:p>
• #### Mechanism of wettability alteration of the calcite {101̄4} surface

(Physical Chemistry Chemical Physics, Royal Society of Chemistry (RSC), 2020-06-29) [Article]
<p>We propose that formation of Na$^{+}$ hydrates plays an important role in the wettability alteration of the calcite {101̄4} surface.</p>
• #### Towards Efficient Neuromorphic Hardware: Unsupervised Adaptive Neuron Pruning

(Electronics, MDPI AG, 2020-06-29) [Article]
<jats:p>To solve real-time challenges, neuromorphic systems generally require deep and complex network structures. Thus, it is crucial to search for effective solutions that can reduce network complexity, improve energy efficiency, and maintain high accuracy. To this end, we propose unsupervised pruning strategies that are focused on pruning neurons while training in spiking neural networks (SNNs) by utilizing network dynamics. The importance of neurons is determined by the fact that neurons that fire more spikes contribute more to network performance. Based on these criteria, we demonstrate that pruning with an adaptive spike count threshold provides a simple and effective approach that can reduce network size significantly and maintain high classification accuracy. The online adaptive pruning shows potential for developing energy-efficient training techniques due to less memory access and less weight-update computation. Furthermore, a parallel digital implementation scheme is proposed to implement spiking neural networks (SNNs) on field programmable gate array (FPGA). Notably, our proposed pruning strategies preserve the dense format of weight matrices, so the implementation architecture remains the same after network compression. The adaptive pruning strategy enables 2.3× reduction in memory size and 2.8× improvement on energy efficiency when 400 neurons are pruned from an 800-neuron network, while the loss of classification accuracy is 1.69%. And the best choice of pruning percentage depends on the trade-off among accuracy, memory, and energy. Therefore, this work offers a promising solution for effective network compression and energy-efficient hardware implementation of neuromorphic systems in real-time applications.</jats:p>
• #### A Robust, Safe and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Environmental Samples

(Cold Spring Harbor Laboratory, 2020-06-29) [Preprint]
<jats:p>Diagnosis and surveillance of emerging pathogens such as SARS-CoV-2 depend on nucleic acid isolation from clinical and environmental samples. Under normal circumstances, samples would be processed using commercial proprietary reagents in Biosafety 2 (BSL-2) or higher facilities. A pandemic at the scale of COVID-19 has caused a global shortage of proprietary reagents and BSL-2 laboratories to safely perform testing. Therefore, alternative solutions are urgently needed to address these challenges. We developed an open-source method called Magnetic- nanoparticle-Aided Viral RNA Isolation of Contagious Samples (MAVRICS) that is built upon reagents that are either readily available or can be synthesized in any molecular biology laboratory with basic equipment. Unlike conventional methods, MAVRICS works directly in samples inactivated in acid guanidinium thiocyanate-phenol-chloroform (e.g., TRIzol), thus allowing infectious samples to be handled safely without biocontainment facilities. Using 36 COVID-19 patient samples, 2 wastewater samples and 1 human pathogens control sample, we showed that MAVRICS rivals commercial kits in validated diagnostic tests of SARS-CoV-2, influenza viruses, and respiratory syncytial virus. MAVRICS is scalable and thus could become an enabling technology for widespread community testing and wastewater monitoring in the current and future pandemics.</jats:p>
• #### Patterns, drivers, and ecological implications of upwelling in coral reef habitats of the southern Red Sea

(Wiley, 2020-06-28) [Preprint]
Coral reef ecosystems are highly sensitive to thermal anomalies, making them vulnerable to ongoing global warming. Yet, a variety of cooling mechanisms, such as upwelling, offer some respite to certain reefs. The Farasan Banks in the southern Red Sea is home to hundreds of coral reefs covering 16,000 km and experiences among the highest water temperatures of any coral-reef region despite exposure to summertime upwelling. We deployed an array of temperature loggers on coral reefs in the Farasan Banks, enabling us to evaluate the skill of satellite-based sea surface temperature (SST) products for capturing patterns of upwelling. Additionally, we used remote sensing products to investigate the physical drivers of upwelling, and to better understand how upwelling modulates summertime heat stress on coral communities. Our results show that various satellite SST products underestimate reef-water temperatures but differ in their ability to capture the spatial and temporal dynamics of upwelling. Monsoon winds from June to September drive the upwelling in the southern Red Sea via Ekman transport of surface waters off the shelf, and this process is ultimately controlled by the southwest Indian monsoon in the Arabian Sea. Further, the timing of the cessation of monsoon winds regulates the maximum water temperatures that are reached in September and October. In addition to describing the patterns and mechanisms of upwelling, our study sheds light on the broad ecological implications of this upwelling system, including modulation of coral bleaching events and effects on biodiversity, sea turtle reproduction, fish pelagic larval duration, and planktivore populations.