bluuebunny/crossref_metadata_2025 huggingface dataset:
Dissipation processes in superconducting NbN nanostructures
Authors: Joshi Lalit M. , Rout P. K. , Husale Sudhir , Gupta Anurag
Published: November 2020

In this paper, we present a comprehensive study of electrical transport measurements on a superconducting film of NbN (thickness, d ∼ 50 nm) and its nanostructures fabricated using Focused Ion Beam (FIB) in the form of one bridge (width, w ∼ 50 µm) and three meanders (w ∼ 500 nm, 250 nm, and 100 nm). The resistance (R) and current–voltage [V(I)] characteristics are measured as a function of temperature (2 K–16 K) and magnetic field (0 T–7 T). The photoresponse is measured under quasi-monochromatic light irradiation (wavelength of ∼800 nm). All our samples with w ≫ ξ and d > ξ are dimensionally on the borderline of the three-dimensional limit. However, the film and bridge samples show quasi-2D signatures of Brzezinski–Kosterlitz–Thouless transition in the R(T) and V(I) characteristics. On the other hand, our meander samples show two slope transitions in R(T) that seem to fit well with the thermally activated phase slip (TAPS) near the superconducting onset and quantum phase slip (QPS) at lower temperatures, expected in quasi-1D superconductors. The presence of TAPS and QPS in all the meander samples is further supported by several other observations at B = 0: (i) linear V(I) at lower excitation currents in the entire transition region; (ii) nonlinear and non-hysteretic V(I) at higher currents in the TAPS region; (iii) in the QPS region, at higher currents, the V(I) curves show a quadratic V ∝ I2 dependence before hysteretic and stepped jumps; and (iv) the switching current (IC*) reduces significantly to 5 μA–25 μA (T = 2 K) when compared to nearly ∼875 μA (T = 10.5 K) in the bridge sample. With the application and increase in the magnetic field, at fixed temperatures in the QPS region of the meander samples, the V(I) characteristics show a crossover to TAPS. This seems to be correlated with a drastic reduction in the activation barrier (Ub) extracted from the R(T,B) data. Typically, for B = 0 T–7 T, Ub varies from ∼3000 K–1200 K (film sample) to ∼1100 K–220 K (bridge sample) and ∼250 K–50 K, ∼150 K–20 K, and ∼50 K–6 K for the 500 nm, 250 nm, and 100 nm meander samples, respectively. Using the Langer, Ambegaokar, McCumber, and Halperin theory [J. S. Langer and V. Ambegaokar, Phys. Rev. 164(2), 498 (1967); D. E. McCumberand B. I. Halperin, Phys. Rev. B 1, 1054 (1970)] and considering the normal state transport properties reported earlier [Joshi et al., AIP Adv. 8, 055305 (2018)], these results are shown to be consistent with disorder induced nano-paths of ∼50 nm, ∼12 nm, ∼10 nm, and ∼7 nm width developed in the FIB fabricated bridge and 500 nm, 250 nm, and 100 nm meander samples, respectively.
Characterization of broadband complex refractive index of synthetic melanin coatings and their changes after ultraviolet irradiation
Authors: Li Weiyao , Patil Anvay , Zhou Xuhao , Wang Zhao , Xiao Ming , Shawkey Matthew D. , Gianneschi Nathan C. , Dhinojwala Ali
Published: November 2020

Melanin, with its high refractive index (RI) and broadband absorption, is an important biomaterial responsible for many of the vibrant structural colors observed in nature and for UV protection. Even though the RI plays an important role in the function of melanin, there is an ambiguity in its reported complex RI and a lack of understanding of whether and how the UV radiation, these materials are likely to experience under normal use, will affect the complex RI. Here, we measured the wavelength-dependent (360–1700 nm) complex RI of synthetic melanin films before and after in situ UV treatment using ellipsometry. We modeled the ellipsometric data using a modified Tauc-Lorentz dispersion model and measured the thickness independently using atomic force microscopy. The UV radiation reduces the film thickness. Interestingly, we find that both the real and imaginary terms of the RI increase upon UV radiation. These experiments provide accurate measurements of the optical properties of melanin and a surprising result that synthetic melanin absorbs more light (∼25% increase in extinction coefficient) below 600 nm after UV exposure.
Study on the oblique water entry impact performance of AUV under different launch conditions based on coupled FEM-ALE method
Authors: Chaudhry Ahmad Zamir , Shi Yao , Pan Guang
Published: November 2020

In this study, the hydrodynamic response of an autonomous underwater vehicle (AUV) subjected to oblique water entry impact is investigated by employing an explicit FEM technique with arbitrary Lagrangian–Eulerian formulation. The predictive ability of the employed numerical model is validated by correlating the cavity evolution of AUV and peak impact accelerations with the experimental outcomes of the previous research work. The influence of advection algorithms on the water entry phenomenon is studied. It is found that the first order donor cell advection scheme is more suitable for low speed impact problems as it is computationally more efficient. However, for high speed water entry simulations, the van Leer advection scheme gives more accurate results. Moreover, using different water entry angles, the effect of the angle of attack (AOA) and length of AUV and its head shape on the impact performances are investigated and discussed. The results show that the radial impact load is more likely to be influenced by AOA and the effect of AOA on the radial impact load is more significant for a small water entry angle, i.e., 30°, as compared to a large entry angle, i.e., 60°. It is also observed that AUV of a smaller length shows the ricochet behavior at a water entry angle of 30°. It is seen that the head shape has a substantial effect on the axial and radial impact loads and velocity attenuation of a vehicle under water. The conclusions drawn in this research work will be beneficial for the selection of appropriate initial launch conditions and for the designing of an AUV structure.
Heterogeneous direct bonding of diamond and semiconductor substrates using NH3/H2O2 cleaning
Authors: Fukumoto Shoya , Matsumae Takashi , Kurashima Yuichi , Takagi Hideki , Umezawa Hitoshi , Hayase Masanori , Higurashi Eiji
Published: November 2020

A diamond (111) substrate cleaned with an NH3/H2O2 mixture could form low-temperature direct bonding under atmospheric conditions. When the diamond surface was bonded with a plasma activated SiO2 surface at 200 °C, the bonding strength was sufficiently high so that cleavage within diamond occurred in a shear test. Moreover, the diamond and Si substrates treated with the NH3/H2O2 mixture could form atomic bonds with a 2.5-nm-thick oxide intermediate layer. This bonding method can be applied to electronic devices using diamond because heterogeneous integration can be achieved using a popular wafer cleaning process followed by low-temperature annealing.
Evaluation of an accurate and consistent mathematical model of an elbow flowmeter derived from the Navier–Stokes equation
Authors: Meng Xianjv , Li Ya , Fan Bingfeng , Li Jian
Published: November 2020

Models derived from the free swirl theory, forced swirl mathematical models, and regression models provide inaccurate predictions of the behavior of elbow flowmeters. To generate an accurate model, we employ the Navier–Stokes equation considering an orthogonal coordinate system according to a curved surface. Thereby, we derive a mathematical model to measure the parameters associated with elbow flowmeters. The effects of physical parameters such as geometric parameters, ratio of bend to diameter, and Reynolds number are investigated. We obtained a relative error below 0.5% upon comparison of the theoretical model calculations and experimental results. This indicates that the proposed model is accurate and useful for future research and industrial production design of elbow flowmeters.
Time-resolved dissociative ionization and double photoionization of CO2
Authors: Bittner Dror M. , Gope Krishnendu , Strasser Daniel
Published: November 2020

CO2 single-photon double photoionization, Coulomb explosion, and dissociative ionization are studied with ultrafast extreme-ultraviolet pump and time-delayed near-infrared probe pulses. Kinetic energy release and momentum correlations for the two-body CO+ + O+ and three-body O+ + C+ + O fragmentation products are determined by 3D coincidence fragment imaging. The transient enhancement of the ratio of two-body vs three-body Coulomb explosion events and the time dependence of low and high kinetic energy release dissociation events are discussed in terms of dissociative ionization and Coulomb explosion dynamics.
Influence of Ga content and high temperature annealing on the short range order and magnetostriction of Fe–Ga single crystals
Authors: Laroche Richard A. , Guruswamy Sivaraman
Published: November 2020

Large magnetostriction observed in Fe–Ga alloys makes them a very important class of alloys for use in a wide range of actuation and sensing applications. This study of quantitative measurements of short-range order (SRO) in a series of Fe–Ga alloys provides valuable insights into the correlations of magnetostrictive responses with an increase in the Ga concentration and annealing. A quantitative assessment of SRO in the first seven shells around an atom in as-grown and high-temperature annealed [001]-oriented Fe–Ga alloy single crystals with Ga contents in the range of 5–20 at. % was carried out using the diffuse peaks in the forbidden (100) peak region of the θ–2θ high-resolution x-ray diffraction pattern. The SRO parameter values obtained indicate that very little short-range ordering occurs in Fe–Ga alloys with low Ga concentrations and ordering is limited to the first few shells. With an increase in Ga content, SRO increases with ordering occurring out to further shells. High temperature annealing decreases SRO parameters to levels approaching random solid solution. The decrease in short-range ordering with high-temperature annealing correlates with the increase in magnetostriction and confirms the hypothesis that the difference in the extent of ordering is the source of the observed high sensitivity of magnetostriction to changes in thermal history.
Contributions to polarization and polarization switching in antiphase boundaries of SrTiO3 and PbZrO3
Authors: Schranz W. , Tröster A. , Rychetsky I.
Published: November 2020

We use a recently developed method—based on layer group analysis combined with the Landau theory—to investigate the polar properties of antiphase boundaries (APBs) in SrTiO3 and PbZrO3. For SrTiO3, we find that, in addition to the biquadratic, Houchmandazeh-Laizerowicz-Salje (HLS) coupling bijklPiPjϕkϕl in the Landau-Ginzburg free energy expansion, additional rotopolar terms of the form WijklPiϕk∂ϕl∂xj contribute considerably to the polarization of antiphase boundaries in these materials. The rotopolar terms can be split into a symmetric flexoelectric part and an antisymmetric one. The antisymmetric Lifshitz term leads to a macroscopic polarization of APBs, which can be switched by application of an external electric field. For PbZrO3, the observed polarization profiles [Wei et al., Mater. Res. Bull. 62, 101 (2015)] are fully compatible with the symmetries of the corresponding layer groups. Unlike in SrTiO3, there exists no Lifshitz invariant WijklPiηk∂ηl∂xj for the order parameter ηi(i=1,…,12) describing the displacements of lead atoms. However, a detailed group theoretical treatment indicates that the polarity of APBs in PbZrO3 is driven by higher order interactions between polarization Pi, order parameter ηk, and order parameter gradients ∂ηl∂xj.
A reactive molecular dynamics study of hyperthermal atomic oxygen erosion mechanisms for graphene sheets
Authors: Cui Zhiliang , Zhao Jin , He Lichao , Jin Haichuan , Zhang Jun , Wen Dongsheng
Published: November 2020

Carbon-based composite materials are widely used in the aerospace field due to their light weight and excellent physical/chemical properties. The mechanisms of the erosion process, e.g., surface catalysis and ablation, during the impact of oxygen atoms, however, remain unclear. In this study, the surface catalysis and ablation behavior during the erosion process of hyperthermal atomic oxygens were achieved through the molecular dynamics method with the reactive force field potential. The concomitant impacts of energy flux density of energetic oxygen atoms, the presence of multiple layers beneath the graphene sheet, and the morphology of graphite surfaces, i.e., graphite basal plane, armchair (AC) edge surface, and zigzag edge surface, respectively, were discussed. The results show that the adsorption of oxygen atoms dominates at the beginning by generating O2 molecules, suggesting the importance of surface catalytic for any ablation study. A unique “layer-by-layer” ablation phenomenon by hyperthermal atomic oxygen is observed for multi-layered graphite slab, and the ablation rate reduces as the number of graphene layers increases. The morphology/structure of the surface shows significant effects on the ablation rate, with AC surfaces showing the largest etching rate and the basal one showing the lowest. The low binding energies of the AC edge are responsible for the difficulty in the formation of stable functional group structures to resist the etching of high-enthalpy oxygen atoms. Such revelation of the detailed surface catalysis and ablation mechanism at the atomistic scale provides insight into design of future materials for the augmentation of the thermal protection effect.
Three-Dimensional CFD Analysis of Hydrodynamics and Mass Transfer in Spacer-Filled RO Channels
Authors: Li Mingheng
Published: November 2020

Hydrodynamics and mass transfer characteristics in the feed channel of the FilmTec BW30-40 spiral wound reverse osmosis (RO) membrane under typical plant operating conditions are investigated using fully coupled three-dimensional computational fluid dynamic (CFD) simulations. It is found that the pressure drop vs average longitudinal velocity follows ΔPc∝u¯1.67. The relationship is nonlinear even under laminar flow conditions because of the existence of spacer filaments. Substantial wall-parallel velocity near the membrane surface is observed, which suppresses boundary layer development. Rolling cells are formed in the center of the feed channel, which promote transverse mixing. Different from concentration polarization phenomenon in unobstructed flat channels, concentrated islands are isolated in regions near spacer filaments where flow is relatively stagnant. The local mass transfer coefficient km oscillates longitudinally but the cell-average k¯m appears fairly constant in cells adjacent to each other. It is shown that k¯m∝u¯0.40 under typical plant operating conditions. A one-dimensional system-level model incorporating the CFD results is developed and validated by plant trial data under various operating conditions, yielding a slight improvement in accuracy as compared to an empirical model.
Hybrid RO-PRO for Energy-Efficient Desalination
Authors: Li Mingheng
Published: November 2020

Specific energy consumptions (SECs) in seawater RO desalination employing staged RO and RO-PRO with energy recovery devices are investigated using systematic mathematical methods. The SECs in both configurations are minimized by solving a constrained nonlinear optimization model which optimally selects operating conditions and allocates membrane area between different membrane units. It is shown that both staged RO and RO-PRO are noticeably advantageous over single-stage RO only if a dimensionless parameter total = A total Lp_0/Q0 is sufficiently large. The RO-PRO outperforms staged RO when internal concentration polarization is not severe, water recovery is low (e.g., 30%) and/or membrane area is abundant (e.g., total _ 1.6). The staged RO is likely to excel at a high water recovery (e.g., 60%) even though the high-salinity brine enhances the driving force for osmotic energy recovery in the RO-PRO. Both configurations have comparable SECs based on water recoveries of 40% and 50% and a total of 0.8, a representative value in industrial seawater RO plants. An multistage RO-PRO (e.g., RO-RO-PRO-PRO) may allow a profile of the applied pressure more closely track that of the concentrate osmotic pressure than RO-PRO, therefore improving energy efficiency. Challenges and opportunities in further development of hybrid RO-PRO processes are discussed.
Interface switch mediates signal transmission in a two-component system
Authors: Wang Mingxing , Guo Qiong , Zhu Kongfu , Fang Bo , Yang Yifan , Teng Maikun , Li Xu , Tao Yuyong
Published: November 2020

Significance

To adapt to the changing environment, bacteria must quickly transduce extracellular information into appropriate cellular response pathways. Two-component systems consisting of a membrane-embedded histidine kinase (HK) and a cytoplasmic response regulator often perform this function. In this work, we present structural and functional data showing that HptRSA, a G6P sensor from
Staphylococcus aureus
, undergoes conformational changes after G6P binding with HptA that causes it to switch its interface with the periplasmic domain of HptS. As a result, a rotation and closure occur in the periplasmic side of the HK. This previously unreported mode of activation not only expands our understanding of HK signal perception in kinase activation but also provides a framework for designing new antimicrobial drugs.
Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion
Authors: Caldwell Shane J. , Haydon Ian C. , Piperidou Nikoletta , Huang Po-Ssu , Bick Matthew J. , Sjöström H. Sebastian , Hilvert Donald , Baker David , Zeymer Cathleen
Published: November 2020

Significance

Despite considerable advances in de novo protein design in recent years, it still remains challenging to engineer proteins with large internal cavities that can be functionalized to become biotechnological tools, such as specific binders, sensors, or catalysts. In this work, we outline a computational strategy to combine multiple de novo designed domains into symmetric protein assemblies that enclose large internal chambers. The high stability of de novo scaffolds enables ready functionalization of these chambers; for instance, with specific metal-binding sites, as demonstrated here by generating a lanthanide-binding protein with ultra-high affinity.
Dissection of the general two-step di-C-glycosylation pathway for the biosynthesis of (iso)schaftosides in higher plants
Authors: Wang Zi-Long , Gao Hao-Meng , Wang Shuang , Zhang Meng , Chen Kuan , Zhang Ya-Qun , Wang Hai-Dong , Han Bo-Yun , Xu Lu-Lu , Song Tian-Qiao , Yun Cai-Hong , Qiao Xue , Ye Min
Published: November 2020

Significance

Schaftoside and isoschaftoside are important plant defense chemicals and bioactive natural products widely present in higher plants. Although a number of plant CGTs have been reported, we know very little about the CGTs catalyzing the biosynthesis of flavonoid di-C-glycosides with different sugar residues. Here we reveal the biosynthesis of (iso)schaftosides in plants is sequentially catalyzed by a pair of homologous but functionally different enzymes (CGTa and CGTb). Crystal structure analysis and key amino acids mutagenesis could switch the function of SbCGTb to SbCGTa. We further reveal this pathway is general for higher plants. Our results provide a platform to efficiently synthesize (iso)schaftosides and to understand their plant defense mechanisms.
Critical point for Bose–Einstein condensation of excitons in graphite
Authors: Wang Jinhua , Nie Pan , Li Xiaokang , Zuo Huakun , Fauqué Benoît , Zhu Zengwei , Behnia Kamran
Published: November 2020

Significance

Bose–Einstein condensation of excitons (pairs of electrons and holes bound by Coulomb attraction) has become a dynamic field of research in the past couple of decades. While individual excitons have been observed in many systems, a collective state of condensed excitons has proved to be more elusive. In this paper, by quantifying the mass and the density of the electron–hole pairs, we identify a critical temperature of 9.2 K and a critical magnetic field of 47 T as the cradle of the Bose–Einstein condensation of excitons in graphite. Our identification radically revises the nature of the field-induced phase transition in graphite and its boundaries.
Exo1 recruits Cdc5 polo kinase to MutLγ to ensure efficient meiotic crossover formation
Authors: Sanchez Aurore , Adam Céline , Rauh Felix , Duroc Yann , Ranjha Lepakshi , Lombard Bérangère , Mu Xiaojing , Wintrebert Mélody , Loew Damarys , Guarné Alba , Gnan Stefano , Chen Chun-Long , Keeney Scott , Cejka Petr , Guérois Raphaël , Klein Franz , Charbonnier Jean-Baptiste , Borde Valérie
Published: November 2020

Significance

Meiotic crossovers are essential for the production of gametes with balanced chromosome content. MutLγ (Mlh1–Mlh3) endonuclease, a mismatch repair heterodimer, also functions during meiosis to generate crossovers. Its activity requires Exo1 as well as the MutSγ heterodimer (Msh4–Msh5). Crossovers also require the polo kinase Cdc5 in a way that is poorly understood. We show that Exo1 directly interacts with Cdc5, and that this promotes the activation of MutLγ for crossovers. Since Cdc5 also controls other key meiotic processes, including kinetochores mono-orientation and disassembly of the synaptonemal complex, this direct interaction with the crossover proteins may be a way to coordinate meiotic chromosome segregation events to avoid untimely activation of the MutLγ endonuclease once recruited to future crossover sites.
Rox8 promotes microRNA-dependent
yki
messenger RNA decay
Authors: Guo Xiaowei , Sun Yihao , Azad Taha , Janse van Rensburg H. J. , Luo Jingjing , Yang Shuai , Liu Peng , Lv Zhongwei , Zhan Meixiao , Lu Ligong , Zhou Yingqun , Ma Xianjue , Zhang Xiaoping , Yang Xiaolong , Xue Lei
Published: November 2020

Significance

Dysregulation of the evolutionarily conserved Hippo pathway has been implicated in multiple diseases including cancer. Here we identified the RNA-binding protein (RBP) Rox8 as a regulator of Hippo signaling-mediated tumorigenesis. Rox8 not only directly binds to the 3′ UTR of
yki
mRNA, but also interacts with miR-8 to recruit miRNA-loaded RISC to degrade
yki
mRNA and therefore impedes Yki-induced tissue growth. We further revealed that TIAR, the human ortholog of Rox8, has retained a conserved regulatory function in
yki
/
YAP
mRNA stability. Our work uncovers a collaborative action of RBP and miRNA in regulating Hippo signaling.
Broad noncoding transcription suggests genome surveillance by RNA polymerase V
Authors: Tsuzuki Masayuki , Sethuraman Shriya , Coke Adriana N. , Rothi M. Hafiz , Boyle Alan P. , Wierzbicki Andrzej T.
Published: November 2020

Significance

Eukaryotic genomes are pervasively transcribed, yet most transcribed sequences lack conservation or known biological functions. We show that a specialized plant-specific RNA polymerase V broadly transcribes the
Arabidopsis
genome. We propose a model where Pol V transcription surveils the genome and is required to recognize and repress newly inserted or reactivated transposons. Our results indicate that pervasive transcription of nonconserved sequences may serve an essential role in maintenance of genome integrity.
Global associations between macronutrient supply and age-specific mortality
Authors: Senior Alistair M. , Nakagawa Shinichi , Raubenheimer David , Simpson Stephen J.
Published: November 2020

Significance

We compiled the most extensive dataset to date of corresponding national macronutrient supplies, survival statistics, and economic data. We show that the national macronutrient supply is a strong predictor of the pattern of mortality in different age classes. Our analyses can show how the optimum macronutrient supply that is predicted to maximize survival changes with age. In early life, equal amounts of fat and carbohydrate are predicted to improve survival. However, as we age, reducing fat in exchange for carbohydrates is associated with the lowest rates of mortality. Our results accord with published experimental and epidemiological data and can help define the mechanisms by which food supply and intake affect public health and demographic processes.
The internal structure and geodynamics of Mars inferred from a 4.2-Gyr zircon record
Authors: Costa Maria M. , Jensen Ninna K. , Bouvier Laura C. , Connelly James N. , Mikouchi Takashi , Horstwood Matthew S. A. , Suuronen Jussi-Petteri , Moynier Frédéric , Deng Zhengbin , Agranier Arnaud , Martin Laure A. J. , Johnson Tim E. , Nemchin Alexander A. , Bizzarro Martin
Published: November 2020

Significance

We discovered a zircon record in a Martian meteorite that spans 4.2 Gyr, nearly the entire geologic history of Mars. Ancient zircons define a bimodal distribution with groupings at 4474 ± 10 Ma and 4442 ± 17 Ma, reflecting intense bombardment episodes triggered by the migration of the gas giant planets. A group of younger detrital zircons record ages from 1548.0 ± 8.8 Ma to 299.5 ± 0.6 Ma. The only plausible sources for these grains are the Elysium and Tharsis volcanic provinces that are the expressions of deep-seated mantle plumes. The chondritic-like Hf-isotope compositions of these zircons require the existence of a primitive and convecting mantle reservoir. Thus, these grains provide a tangible record of the deep Martian interior.
The intracellular Ca
2+
release channel TRPML1 regulates lower urinary tract smooth muscle contractility
Authors: Griffin Caoimhin S. , Alvarado Michael G. , Yamasaki Evan , Drumm Bernard T. , Krishnan Vivek , Ali Sher , Nagle Eleanor M. , Sanders Kenton M. , Earley Scott
Published: November 2020

Significance

TRPML1 (transient receptor potential mucolipin 1) is a Ca
2+
-permeable, nonselective cation channel that is localized to late endosomes and lysosomes. Here, we investigated the function of TRPML1 channels in regulating lower urinary tract (LUT) smooth muscle cell (SMC) contractility. We found that TRPML1 forms a stable signaling complex with ryanodine receptors (RyRs) in the sarcoplasmic reticulum (SR). We further showed that TRPML1 channels are important for initiating an essential Ca
2+
-signaling negative feedback mechanism between RyRs on SR membranes and K
+
channels on the plasma membrane. Knockout of TRPML1 channels in mice impaired this pathway, resulting in LUT smooth muscle hypercontractility and symptoms of overactive bladder. Our findings demonstrate a critical role for TRPML1 in LUT function.
Structure-function analysis of microRNA 3′-end trimming by Nibbler
Authors: Xie Wei , Sowemimo Ivica , Hayashi Rippei , Wang Juncheng , Burkard Thomas R. , Brennecke Julius , Ameres Stefan L. , Patel Dinshaw J.
Published: November 2020

Significance

We report on structure-function studies of the conserved 3′-to-5′ exoribonuclease Nibbler (Nbr) toward understanding its role in 3′-end trimming of small regulatory RNAs. Our studies of the Nbr N-terminal domain provide insights into its role as a double-strand RNA-binding recruitment platform that is required for Nbr-directed microRNA trimming and that experimentally can be bypassed through an Argonaute-interacting peptide. Structural studies on Nbr’s exonucleolytic domain suggest a substrate selectivity of the Mn
2+
-coordinated DEDDy catalytic domain toward non–2′-
O
-methylated small RNAs. Our findings provide conceptual insights into how Nbr participates in small RNA biogenesis.
A chemical dynamics study on the gas-phase formation of triplet and singlet C
5
H
2
carbenes
Authors: He Chao , Galimova Galiya R. , Luo Yuheng , Zhao Long , Eckhardt André K. , Sun Rui , Mebel Alexander M. , Kaiser Ralf I.
Published: November 2020

Significance

Carbenes represent key reactive intermediates in molecular mass growth processes leading to carbonaceous nanostructures in the interstellar medium and in combustion systems. However, due to their short lifetimes and tendency for dimerization, carbenes represent one of the foremost obscured classes of reactive intermediates, with the preparation of carbenes in the gas phase remaining largely elusive. By merging molecular beams with electronic structure and quasi-classical trajectory calculations and exploiting triplet pentadiynylidene (HCCCCCH) and singlet ethynylcyclopropenylidene (c-C
5
H
2
) carbene as benchmarks, we present a versatile protocol to unravel the dynamics leading to exotic carbenes under single-collision conditions. These elementary mechanisms are of significance to our understanding of the fundamental processes leading to unsaturated organic transients in extreme, hydrocarbon-rich environments.
An S/T motif controls reversible oligomerization of the Hsp40 chaperone DNAJB6b through subtle reorganization of a β sheet backbone
Authors: Karamanos Theodoros K. , Tugarinov Vitali , Clore G. Marius
Published: November 2020

Significance

Some of the most potent chaperones that protect against protein aggregation form heterogeneous oligomers that are crucial for function. Due to the polydisperse nature of these oligomers, the molecular origins that drive self-assembly remain poorly understood. Here, using a predominantly monomeric construct of the C-terminal domain of DNAJB6b we reveal an interplay between two N-terminal β strand configurations which we analyze quantitatively in structural and kinetic terms. We show that the two backbone conformations impact the assembly state of the C-terminal domain, with one being essentially monomeric and the other prone to oligomerization. The same residues in full-length DNAJB6b are vital for antiaggregation activity and thus we hypothesize that the equilibria characterized here lie at the core of DNAJB6b function.
Analysis of end‐spurt behaviour in elite 800‐m and 1500‐m freestyle swimming
Authors: Neuloh Joshua E. , Skorski Sabrina , Mauger Lex , Hecksteden Anne , Meyer Tim
Published: November 2020

To analyse the influence of distance, time point of competition, round and finishing position on end‐spurt behaviour in swimming. Race results in 800‐m and 1500‐m freestyle swimming from the last 8 World Championships and 5 Olympic Games (1998–2016) including 1433 races and 528 swimmers were obtained. The end‐spurt for each race was determined by means of an End‐Spurt Indicator (ESI). The ESI was calculated by dividing the difference between the swim velocity of the last lap (SVLL) and the mean swim velocity of the middle part of the race (SVMP) by the respective individual standard deviation of SVMP. Subsequently, ESI was used as a dependent variable and influences were analysed using a linear mixed model with fixed effects for distance, time point of competition, round and finishing position. An end‐spurt was evident in most swims for both race distances. The mean change in swim velocity between the middle part of the race and the last lap was 0.06 ± 0.02 m/s (1.2 ± 0.2 s) in the 800‐m and 0.07 ± 0.02 m/s (1.5 ± 0.2 s) in the 1500‐m. The finishing position within a race significantly affected the ESI (P < .001, t = 7.28). Specifically, when analysing finals only, ESI was significantly greater in medallists (5.76; quantile: 3.61 and 8.06) compared to non‐medallists (4.06; quantile: 1.83 and 6.82; P = .001). The between‐subject standard deviation was 1.66 (Cl: 1.42–1.97) with a relative variance component of 23%, while 77% of ESI variance remained unexplained. This is the first study using a newly developed indicator of end‐spurt behaviour demonstrating that particularly medallists have a more pronounced end‐spurt compared to non‐medallists.
Validation of a new open-source method for automatic delineation and dose assessment of the heart and LADCA in breast radiotherapy with simultaneous uncertainty estimation
Authors: Finnegan Robert , Laugaard Lorenzen Ebbe , Dowling Jason , Thwaites David , Delaney Geoff , Brink Carsten , Holloway Lois
Published: November 2020

Radiotherapy has been shown to increase risks of cardiotoxicities for breast cancer patients. Automated delineation approaches are necessary for consistent and efficient assessment of cardiac doses in large, retrospective datasets, while patient-specific estimation of the uncertainty in these doses provides valuable additional data for modelling and understanding risks. In this work, we aim to validate the consistency of our previously described open-source software model for automatic cardiac delineation in the context of dose assessment, relative to manual contouring. We also extend our software to introduce a novel method to automatically quantify the uncertainty in cardiac doses based on expected inter-observer variability (IOV) in contouring. This method was applied to a cohort of 15 left-sided breast cancer patients treated in Denmark using modern tangential radiotherapy techniques. On each image set, the whole heart and left anterior descending coronary artery (LADCA) were contoured by nine independent experts; the range of doses to these nine volumes provided a reference for the dose uncertainties generated from the automatic method. Local and external atlas sets were used to test the method. Results give confidence in the consistency of automatic segmentations, with mean whole heart dose differences for local and external atlas sets of −0.20 ± 0.17 and −0.10 ± 0.14 Gy, respectively. Automatic estimates of uncertainties in doses are similar to those from IOV for both the whole heart and LADCA. Overall, this study confirms that our automated approach can be used to accurately assess cardiac doses, and the proposed method can provide a useful tool in estimating dose uncertainties.
Characterizing blood clots using acoustic radiation force optical coherence elastography and ultrasound shear wave elastography
Authors: Liu Hsiao-Chuan , Abbasi Mehdi , Ding Yong Hong , Roy Tuhin , Capriotti Margherita , Liu Yang , Fitzgerald Seán , Doyle Karen M , Guddati Murthy , Urban Matthew W , Brinjikji Waleed
Published: November 2020

Thromboembolism in a cerebral blood vessel is associated with high morbidity and mortality. Mechanical thrombectomy (MT) is one of the emergenc proceduresperformed to remove emboli. However, the interventional approaches such as aspiration catheters or stent retriever are empirically selected. An inappropriate selection of surgical devices can influence the success rate during embolectomy, which can lead to an increase in brain damage. There has been growing interest in the study of clot composition and using a priori knowledge of clot composition to provide guidance for an appropriate treatment strategy for interventional physicians. Developing imaging tools which can allow interventionalists to understand clot composition could affect management and device strategy. In this study, we investigated how clots of different compositions can be characterized by using acoustic radiation force optical coherence elastography (ARF–OCE) and compared with ultrasound shear wave elastography (SWE). Five different clots compositions using human blood were fabricated into cylindrical forms from fibrin-rich (21% red blood cells, RBCs) to RBC-rich (95% RBCs). Using the ARF–OCE and SWE, we characterized the wave velocities measured in the time-domain. In addition, the semi-analytical finite element model was used to explore the relationship between the phase velocities with various frequency ranges and diameters of the clots. The study demonstrated that the wave group velocities generally decrease as RBC content increases in ARF–OCE and SWE. The correlation of the group velocities from the OCE and SWE methods represented a good agreement as RBC composition is larger than 39%. Using the phase velocity dispersion analysis applied to ARF–OCE data, we estimated the shear wave velocities decoupling the effects of the geometry and material properties of the clots. The study demonstrated that the composition of the clots can be characterized by elastographic methods using ARF–OCE and SWE, and OCE demonstrated better ability to discriminate between clots of different RBC compositions, compared to the ultrasound-based approach, especially in clots with low RBC compositions.
Generation of a noise-like pulse from an erbium-doped fiber laser based on nonlinear multimode interference
Authors: Zhao Fengyan , Li Ning , Wang Hushan
Published: November 2020

A noise-like pulse (NLP) is generated in an anomalous-dispersion passively mode-locked erbium-doped fiber laser using graded-index multimode fiber (GIMF) as the all-fiber saturable absorber (SA) for the first time. By splicing two sections of bending GIMF at both ends of a single mode fiber and optimizing the birefringence and nonlinear parameters, stable NLP mode-locking operation can be achieved within a wide pump power range. Meanwhile, the performances of NLP mode-locking have been analyzed experimentally by changing the length of the GIMF.
Evaluation of Strength Deterioration Factor on Blended Concrete Exposed to Magnesium Sulphate Solution
Authors: Jena Trilochan , Chandra Panda Kishor , Panda Chittaranjan
Published: November 2020

This paper reports the combined effects of industrial waste as fly ash (FA) and agro-waste such as silpozz on the compressive strength and strength deterioration factor (SDF) of blended cement concrete exposed to 5% and 10% MgSO4 solution and normal water. Silpozzis manufactured by burning of agro-waste rice husk in designed furnace in between 600° to 700°C which is one of the main agriculture.al residues obtained from the outer covering of rice grains during the milling process. There are four mix series taken with control mix. The control mix made 0% replacement of FA and silpozz with Ordinary Portland Cement (OPC). The first mix series made 0% FA and 10-30% replacement of silpozz with OPC. The second mix series made with 10% FA and 10-40% replacement of silpozz with OPC. The third mix series made 20% FA and 10-30% replacement of silpozz with OPC and the fourth mix series made 30% FA and 10-20% silpozz replaced with OPC. The samples (cubes) are prepared and cured in normal water and 5% and 10% MgSO4 solution for 7, 28 and 90 days. The studied parameters are compressive strength and strength deterioration factor (SDF) for 7, 28 and 90 days. The regression equations and value of correlation coefficient R2 between compressive strength and partial replacement of silpozz is obtained and revealed from these results that value of correlation coefficient is varied from 0.9602 to 1.
Advances in Seismic Strengthening Materials and Techniques
Authors: Mahadik Sanjivan , Mahajan Lomesh , Bhagat S. R.
Published: November 2020

Seismic strengthening of reinforced concrete (RC) members is a method of improving their existing capacity to withstand seismic forces. The process typically includes strengthening of RC structural members such beams, columns, slabs, footings, beam-column junctions, etc. to improve the axial, flexure, and shear capacity. Experiences during the recent earthquakes and changes in Indian Standards made it essential to carry out structural audit of buildings. The buildings, which do not comply with the recent Code provisions have to be reconstructed or to be strengthened to achieve the desired capacity level. Reconstruction of such buildings will consume time and money. In addition, evacuation of such buildings for reconstruction is a difficult task. In this paper an attempt has been made to focus on the seismic strengthening of structural members of RC buildings which are designed to only gravity loads or the structures designed prior to release of new building Codes. This paper covers a brief introduction of conventional methods of strengthening followed by an introduction of advanced FRP composite materials and techniques of retrofitting for existing RC buildings. Finally, it is concluded that the advanced FRP composite materials and recent innovative methods can more advantageously used for seismic strengthening of RC buildings.
Characterization of Alkali Activated Bentonite - Fly Ash as Brick Material
Authors: Rout P P , Garanayak L
Published: November 2020

Brick, one of the most common binding materials which need excess energy during manufacture. Gathering of excess industrial waste creates the environmental pollution as well as a health issue. To developing green environment, industrial waste can be used as an alternation of binder material as a brick. In this present study combination of sodium bentonite and fly ash get activated by sodium hydroxide (NaOH) and calcium oxide (CaO) whose Na2O/CaO proportion varied as 1 with mole content. Mixing proportion of both solid particles were varied as 40/60 and 60/40 as weight percentages. Casted samples were conducted for the curing period of 0 days, 3 days, 7 days, and 28 days. Mineralogy, morphology, and compressive strength tests are conducted and found that 1.5 moles are the best for developing compressive strength that obtained as 135.8 kPa at 60°C oven curing temperature.
Impact of Ultrafine Ground Granulated Blast Furnace Slag on the Properties of High Strength Durable Concrete
Authors: Sethy Kaliprasanna , Rojalin Nanda S
Published: November 2020

Ultrafine ground granulated blast furnace slag (UFGGBFS), because of its pozzolanic nature, could be an extraordinary resource for the advanced development needs, since slag cements concrete can be of elite, if properly planned. Improvement of the durability properties of concrete to support a more extended life expectancy and creating a climate amicable greener concrete are turning out to be significant standards in getting high quality concrete. Fusing Ultrafine Ground Granulated Blast Furnace Slag (UFGGBFS) as a mineral admixture enhances the workability of fresh concrete and decreased the link between pores; in this way, decreasing the permeability and improving the obstruction of the solid against chloride infiltration. The measure of ozone depleting substance delivered in making the concrete and the energy needed to create the concrete are significantly decreased with the utilization of UFGGBFS. Ultrafine GGBFS (UFGGBFS) with a normal molecule size less than 10m and a Blaine surface area more than 600m2/kg can significantly improve the properties of the concrete as far as diffusion and chemical reactivity impacts. Compared with GGBFS, the UFGGBFS increases the rate of hydration and pozzolanic responses and has a superior filling impact. In this study, the early development of mechanical strength and permeability properties of high strength concrete with UFGGBFS is examined. Total five mixes with 180kg/m3 each of both Ordinary Portland Cement (OPC) concrete and Ultrafine Ground Granulated Blast furnace Slag (UFGGBFS) concrete were designed. The mixes starts from 0% replacement and gradually increases up to 20% (i.e 0, 5, 10, 15 and 20%) of identical all total cementitious materials with UFGGBFS substitution were planned and a sum of 145 samples from the five blends were projected. Compressive strength parameters, flexural strength parameter, modulus of elasticity parameter and water permeability test outcomes are introduced.
Stress-Strain Behaviour of Compacted Pond Ash Reinforced with Stone Column
Authors: Naik J K
Published: November 2020

Ash pond deposits are characterized by its high compressibility and low bearing capacity which is unappropriated for the construction of engineering structures over it. There are several techniques to improve the bearing capacity of ash deposits. Stone column is one of the effective techniques employed to increase the bearing capacity for construction of engineering structures over soft soil deposits. Stone columns are extensively used to improve the bearing capacity of poor ground, time rate of settlements, stiffness, reduce the settlement of structure, and liquefaction potential of soft ground. This paper reports the load settlement behaviour of compacted pond ash beds reinforced with stone columns. Both end bearing and floating stone columns of different length ratios and area ratios were introduced in compacted pond ash beds having different densities. The load-settlement behaviour of footings supported on different configurations of stone columns was studied.
Sensitive detection of water/oxygen molecule adsorption and reaction on a titanium oxide nanosheet with a graphene field effect transistor
Authors: Yoshida Yuhsuke , Imafuku Tatsuya , Inoue Daiki , Uechi Seita , Shite Daiki , Katsuki Yuhto , Funatsu Asami , Shimojo Fuyuki , Hara Masahiro
Published: November 2020

We have investigated molecule adsorption phenomena on a chemically active surface of titanium oxide nanosheet by coupling with an electrically sensitive graphene field effect transistor (FET). Super-hydrophilic surface of the titanium oxide nanosheet forms a water-layer in ambient air which exhibits a large hysteresis of drain current in the hybrid FET for sweeping gate-voltage. The large hysteresis disappears in vacuum, which indicates physically adsorbed water molecules on the surface of the titanium oxide nanosheet dominantly contribute to the hysteresis. UV light irradiation in vacuum significantly changes the drain current due to desorption of the adsorbed molecules. Sufficient UV irradiation results in symmetric gate-voltage dependence similar to those of conventional graphene FETs. Exposure to an oxygen gas atmosphere leads to a heavy hole doping in the FET, where the binding of the oxygen molecules is stronger than that of water molecules. In a humidified nitrogen atmosphere, a large shift of charge neutrality point is observed in transfer characteristics crossing between electron doping and hole doping. By contrast, a clear square-shaped hysteresis loop is observed in a humidified oxygen atmosphere, where the hole density in the graphene drastically changed with O2/H2O redox couple reaction on the titanium oxide nanosheet.
How to Optimize Aesthetics for the Partial Mastectomy Patient
Authors: Losken Albert , Brown Ciara A
Published: November 2020

Aesthetic concern is one of the main driving forces behind the popularity of the oncoplastic approach to breast conservation therapy. Oncoplastic options at the time of lumpectomy include volume replacement techniques such as flaps and volume displacement techniques such as the oncoplastic reduction. These techniques can be employed to ensure preservation of breast shape and contour, size and symmetry, inframammary fold position, and position of the nipple-areola complex. The importance of aesthetic outcomes is not only to improve overall patient satisfaction but also to minimize the need for revisional surgeries for shape and symmetry. The purpose of this review is to discuss ways to optimize the aesthetic result and to review the evidence behind aesthetic outcomes.
IMIX: a multivariate mixture model approach to association analysis through multi-omics data integration
Authors: Wang Ziqiao , Wei Peng
Published: November 2020

Motivation

Integrative genomic analysis is a powerful tool used to study the biological mechanisms underlying a complex disease or trait across multiplatform high-dimensional data, such as DNA methylation, copy number variation and gene expression. It is common to perform large-scale genome-wide association analysis of an outcome for each data type separately and combine the results ad hoc, leading to loss of statistical power and uncontrolled overall false discovery rate (FDR).

Results

We propose a multivariate mixture model (IMIX) framework that integrates multiple types of genomic data and allows modeling of inter-data-type correlations. We investigated the across-data-type FDR control in IMIX and demonstrated lower misclassification rates at controlled overall FDR than established individual data type analysis strategies, such as the Benjamini–Hochberg FDR control, the q-value and the local FDR control by extensive simulations. IMIX features statistically principled model selection, FDR control and computational efficiency. Applications to The Cancer Genome Atlas data provided novel multi-omics insights into the genes and mechanisms associated with the luminal and basal subtypes of bladder cancer and the prognosis of pancreatic cancer.

Availabilityand implementation

We have implemented our method in R package ‘IMIX’ available at https://github.com/ziqiaow/IMIX, as well as CRAN soon.

Supplementary information

Supplementary data are available at Bioinformatics online.