bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of fluorine on the suppression of boron diffusion in pre-amorphized silicon
Authors: Kiga Ryotaro , Uematsu Masashi , Itoh Kohei M.
Published: September 2020

The effect of fluorine (F) on diffusion of boron (B) in silicon (Si) is investigated by secondary ion mass spectrometry of Si, B, and F diffusion using pre-amorphized natSi/28Si isotope multilayers that are co-implanted with B and F. By the presence of F, diffusion of B is suppressed while that of Si is enhanced. A quantitative analysis of the experimental results based on our diffusion model shows that the suppression of B diffusion is due to (1) Si interstitial undersaturation caused by the time-dependent formation and dissolution of F-vacancy (FV) clusters and (2) direct interaction between B and FV clusters. The model developed in this study enables an accurate simulation of B and Si diffusion in the presence of F in Si.
Thermodynamic or density scaling of the thermal conductivity of liquids
Authors: Harris Kenneth R.
Published: September 2020

Thermodynamic or density scaling is applied to thermal conductivity (λ) data from the literature for the model Lennard-Jones (12-6) fluid; the noble gases neon to xenon; nitrogen, ethene, and carbon dioxide as examples of linear molecules; the quasi-spherical molecules methane and carbon tetrachloride; the flexible chain molecules n-hexane and n-octane; the planar toluene and m-xylene; the cyclic methylcyclohexane; the polar R132a and chlorobenzene; and ammonia and methanol as H-bonded fluids. Only data expressed as Rosenfeld reduced properties could be scaled successfully. Two different methods were used to obtain the scaling parameter γ, one based on polynomial fits to the group (TVγ) and the other based on the Avramov equation. The two methods agree well, except for λ of CCl4. γ for the thermal conductivity is similar to those for the viscosity and self-diffusion coefficient for the smaller molecules. It is significantly larger for the Lennard-Jones fluid, possibly due to a different dependence on packing fraction, and much larger for polyatomic molecules where heat transfer through internal modes may have an additional effect. Methanol and ammonia, where energy can be transmitted through intermolecular hydrogen bonding, could not be scaled. This work is intended as a practical attempt to examine thermodynamic scaling of the thermal conductivity of real fluids. The divergence of the scaling parameters for different properties is unexpected, suggesting that refinement of theory is required to rationalize this result. For the Lennard-Jones fluid, the Ohtori–Iishi version of the Stokes–Einstein–Sutherland relation applies at high densities in the liquid and supercritical region.
Heat transport in semiconductor crystals: Beyond the local-linear approximation
Authors: Ezzahri Younès , Joulain Karl , Ordonez-Miranda José
Published: September 2020

We extend the application of the nonlocal theory of Mahan and Claro [Phys. Rev. B 38, 1963 (1988)] to solve the steady-state Boltzmann–Peierls transport equation within the framework of the single mode relaxation time approximation using the modified Debye–Callaway model. We consider the case of a semi-infinite semiconductor (SC) crystal with a boundary condition at its top surface that can be considered reasonably representative of time domain thermoreflectance (TDTR) and frequency domain thermoreflectance (FDTR) techniques. The approach allows us to obtain three different contributions to the heat flux density current that shed further light on the fundamental role of nonlocality and nonlinearity in heat transport by phonons in SC crystals. Through their intrinsic and implicit shuffling effect of the crystal momentum, phonon–phonon Normal scattering processes play a key role in the onset of thermal conduction as they introduce the temperature Laplacian as a second driving potential force for the heat flux density current in addition to the conventional Fourier's temperature gradient. The developed model suits quite fairly to interpret the frequency behavior of the reduced effective thermal conductivity of SC crystals that is observed in TDTR and FDTR experiments. We obtain an expression of the effective thermal conductivity of the SC crystal that is characterized with a universal spectral suppression function that captures and describes the role, the weight, and the contribution of quasi-ballistic and non-diffusive phonons. The spectral suppression function only depends on the ratio between the phonon mean free path and the thermal penetration depth as defined based on the diffusive Fourier's law.
Correlation analysis among multiple images of plasma induced during fiber laser–arc hybrid welding
Authors: Zou Jianglin , Wang Lida , Xiao Rongshi
Published: September 2020

In this study, the multiple imaging morphological features of plasma have been observed by using the multiple-imaging technique during the fiber laser–tungsten insert gas (TIG) arc hybrid welding. Four images of the plasma can be simultaneously obtained in a picture. From the first image to the fourth image, there is a gradual decrease in area and a gradual increase in light intensity. The first three images have approximately consistent time-dependent area changes. This consistency and the stability of the first three images increase with the increase in the arc current or with the decrease in the heat source spacing or laser power. The third image has a higher area fluctuation frequency than the first image. The metal vapor and the shielding gas are not fully mixed, and the fluctuation of the metal plasma is the main cause of the hybrid welding plasma fluctuation.
Dynamic behavior and maximum spreading of droplets impacting concave spheres
Authors: Liu Xin , Min Jingchun , Zhang Xuan
Published: September 2020

Droplet impact is omnipresent in nature and industry, and it is affected by the surface shape. Here, experiments, simulations, and theoretical analyses are conducted to explore the impact behaviors of water droplets on the concave spheres, especially the maximum spreading. The simulation model using the volume of fluid method is validated by comparing the temporal droplet profiles and spreading factors yielded by the simulation and experiment. The effects of the Weber number, contact angle, and sphere-to-droplet diameter ratio on the maximum spreading are exhaustively investigated. The results indicate that both the maximum spreading factor and arc angle increase with the increase in the Weber number and the decrease in the contact angle. The maximum spreading factor and area on the concave sphere generally first increase slightly and then decrease with the reduction in the diameter ratio owing to the combined action of the gravity and the surface shape. As the diameter ratio decreases, the maximum spreading arc angle increases and the maximum diameter of the contact line decreases. For a fixed diameter ratio, the droplet generally spreads less on a concave surface than on a convex one. Based on the energy conservation, a theoretical model is further established to predict the changing trend of the maximum spreading factor with the Weber number, contact angle, and diameter ratio, which yields a ±15% deviation over 93% of all the data points. This work may deepen our understanding of the mechanism of droplet impact on concave spheres and contribute to the associated applications.
Shear localization in molecular crystal cyclotetramethylene-tetranitramine (β-HMX): Constitutive behavior of the shear band
Authors: Khan Mohammad , Picu Catalin R.
Published: September 2020

The energetic molecular crystal cyclotetramethylene-tetranitramine (HMX) is used in plastic bonded explosives, and reaction initiation and detonation are usually triggered by plastic deformation. However, the mechanism of plastic deformation in β-HMX, which is the HMX phase stable in ambient conditions, is still a matter of debate. A recent observation that pressure developing under shock conditions inhibits dislocation activity, leaves shear localization as the main deformation mechanism in this crystal at high pressures and strain rates. In this work, the steady state shear band viscosity is evaluated as a function of the applied pressure, temperature, and shear strain rate using atomistic models of the HMX crystal. The viscosity of a fully formed shear band decreases as a power function of the strain rate and decreases linearly with increasing temperature, demonstrating shear thinning and non-Arrhenius behavior. The viscosity increases with increasing pressure. The fully formed band behavior is independent of the crystallographic orientation. It is shown that viscosity can be expressed exclusively in terms of the density of the non-crystalline material in the band, and hence the results can be explained in terms of the excess free volume theory developed for shear bands in other material systems, e.g., metallic glasses. The stress required to nucleate a shear band from a straight pre-existing dislocation is reported as a function of the applied pressure, temperature, and strain rate.
Convolutional neural network based hierarchical autoencoder for nonlinear mode decomposition of fluid field data
Authors: Fukami Kai , Nakamura Taichi , Fukagata Koji
Published: September 2020

We propose a customized convolutional neural network based autoencoder called a hierarchical autoencoder, which allows us to extract nonlinear autoencoder modes of flow fields while preserving the contribution order of the latent vectors. As preliminary tests, the proposed method is first applied to a cylinder wake at ReD = 100 and its transient process. It is found that the proposed method can extract the features of these laminar flow fields as the latent vectors while keeping the order of their energy content. The present hierarchical autoencoder is further assessed with a two-dimensional y–z cross-sectional velocity field of turbulent channel flow at Reτ = 180 in order to examine its applicability to turbulent flows. It is demonstrated that the turbulent flow field can be efficiently mapped into the latent space by utilizing the hierarchical model with a concept of an ordered autoencoder mode family. The present results suggest that the proposed concept can be extended to meet various demands in fluid dynamics including reduced order modeling and its combination with linear theory-based methods by using its ability to arrange the order of the extracted nonlinear modes.
Systematic revision of the Indo-West Pacific colourful bubble-snails of the genus Lamprohaminoea Habe, 1952 (Cephalaspidea : Haminoeidae)
Authors: Oskars Trond R. , Malaquias Manuel António E.
Published: September 2020

The genus Lamprohaminoea includes species of colourful haminoeid snails associated with coral reefs and rocky shores in the tropical Indo-West Pacific. In this work, we revise the diversity and systematics of Lamprohaminoea species based on a phylogenetic hypothesis and on a detailed morphological analysis of specimens. Shells, external features of the animals and anatomical characters from the jaws, radula, gizzard plates, and male reproductive system were studied by optical and scanning electron microscopy. Additionally, a molecular species delimitation analysis based on the Automatic Barcode Gap Discovery method using DNA sequences of the cytochrome c oxidase subunit I was implemented. Five species were recognised, three of them new to science, namely L. cymbalum, L. ovalis, L. vamiziensis sp. nov., L. evelinae sp. nov., and L. mikkelsenae sp. nov. Morphologically, these species can be separated by subtle differences of their external colouration and by features of the male reproductive system. Lamprohaminoea vamiziensis sp. nov. is known only from the western Indian Ocean and L. evelinae sp. nov., from the west Pacific, whereas the other three occur across the Indo-West Pacific realm.
Molecular phylogenetics disentangles the limits of a group of related Neotropical doryctine parasitoid wasp genera (Hymenoptera : Braconidae)
Authors: Gadelha Sian de Souza , Zaldívar-Riverón Alejandro , de Oliveira Marcio Luiz
Published: September 2020

The Doryctinae is one of the most specious subfamilies of the mainly parasitoid wasp family Braconidae. Members of this subfamily are characterised by having a very heterogeneous external morphology, which has made establishing the limits of several of its genera extremely difficult. The Neotropical Callihormius Ashmead, Platydoryctes Barbalho & Penteado-Dias, and Aphelopsia Marsh are prime examples of this, since they show extensive interspecific morphological variation but lack consistent diagnostic features among them. We carried out a comprehensive phylogenetic study among several representative species belonging to the above genera as well as other morphologically similar doryctine taxa based on three nuclear and two mitochondrial (mt)DNA sequence markers. Based on the relationships recovered, we assessed the generic limits among the examined taxa and investigated the times of origin and diversification in this group. Our best estimate of phylogeny did not recover Callihormius as monophyletic, and thus we propose a taxonomic arrangement where we elevate the status of Ca. (Dmitriohormius) Belokobylskij, Zaldívar-Riverón & Coronado-Blanco to genus level, stat. nov., and also describe four new genera: Macrometasoma, gen. nov., Caputlenis, gen. nov., Platyhormius, gen. nov. and Caputrugosus, gen. nov. Platydoryctes is delimited morphologically, and the body flatness is proposed to have independently evolved more than once within the group of genera examined. Aphelopsia was not recovered as monophyletic, though the relationships involved were weakly supported and therefore we maintain its species composition. Panama Marsh, stat. rev., which was considered a junior synonym of Leluthia Cameron, is resurrected. Basal relationships in the phylogeny had very short branch lengths, which could be due to ancient rapid radiation events that occurred during the early evolution of the group. The estimated times of divergence showed that the clade containing Callihormius and its related genera originated between the late Oligocene and middle Miocene, whereas its early diversification events probably occurred between the middle to late Miocene.
Current status of pharmacy services in primary healthcare institutions in Jiangsu Province, China
Authors: Huang Yuankai , Yao Dongning , Xi Xiaoyu , Wang Yitao , Yao Wenbing
Published: September 2020

China is attempting to establish a pharmacy services network in primary healthcare (PHC) institutions. This study investigated the current status of pharmacy services in China. Following a conceptual framework derived from the structure–process–outcome model, a questionnaire was sent to a sample of 700 administrators, 2000 GPs, 2000 pharmacy service providers, 2000 patients with chronic diseases and 2000 patients receiving antibiotic transfusion treatment, selected using a multistage sampling strategy, from PHC institutions in Jiangsu Province, China, in July and August 2016. The installation of pharmaceutical facilities and devices, staffing by pharmaceutical professionals, patterns of pharmacy service provision and the outcomes of these services were assessed using descriptive statistics. There were 8346 respondents from 665 institutions (response rate 95.9%). Pharmaceutical department (63.0%), dispensary (50.2%) and pharmacy intravenous admixture services (54.1%) were not established in many PHC institutions. Dispensing (22.9%), pharmacotherapy consultation for patients (19.3%), drug management (17.4%) and prescription checking (16.5%) were the most important tasks for pharmacy service providers. Patients reported lower satisfaction with the dissemination of information regarding medication use (mean (±s.d.) 8.85±1.00%), the treatment of adverse drug reactions (5.65±0.50%), medical insurance reimbursement (15.25±2.45%) and the convenience of buying drugs (6.35±0.65%). Several issues regarding the facilities and devices related to pharmacy services, the quality and responsibilities of pharmacy service providers and the outcomes of pharmacy services may hamper the development of a pharmacy service system in PHC in China.
Practice nurses and providing preconception care to women in Australia: a qualitative study
Authors: Walker Ruth , Kandel Pragya , Hill Briony , Hills Sharon , Dunbar James , Skouteris Helen
Published: September 2020

The aims of this study were to explore women’s and health professionals’ perspectives of preconception care and whether expanding the role of practice nurses (PNs) to provide preconception care is acceptable. In a descriptive qualitative approach, 23 semistructured interviews and three focus groups were conducted with women (n=14), PNs (n=8), GPs (n=10) and practice managers (n=2) in the state of Victoria, Australia, between September and December 2019. An inductive process of thematic analysis identified five themes and 12 subthemes. Women and health professionals viewed preconception to be when a woman is planning a pregnancy. Women wanted personalised preconception care, and receiving this from a PN was considered to be acceptable. If the role of PNs is expanded, PNs would require training and professional recognition of their role to provide preconception care. Funding barriers were discussed by PNs, GPs and practice managers, along with potential solutions, such as Medicare item numbers and checklists to streamline consultations. Other resources in the wider community, such as schools, were identified as important aspects of a coordinated approach. Overall, expanding the role of PNs to provide preconception care was acceptable to women and health professionals to increase women’s awareness and uptake of preconception care.
Strong spatial embedding of social networks generates nonstandard epidemic dynamics independent of degree distribution and clustering
Authors: Haw David J. , Pung Rachael , Read Jonathan M. , Riley Steven
Published: September 2020

Significance

Epidemics are typically described using a standard set of mathematical models that do not capture social interactions or the way those interactions are determined by geography. Here, we propose a model that can reflect social networks influenced strongly by the way people travel, and we show that they lead to very different epidemic profiles. This type of model will likely be useful for forecasting.
Thermoelectric response from grain boundaries and lattice distortions in crystalline gold devices
Authors: Evans Charlotte I. , Yang Rui , Gan Lucia T. , Abbasi Mahdiyeh , Wang Xifan , Traylor Rachel , Fan Jonathan A. , Natelson Douglas
Published: September 2020

Significance

Scanning photothermoelectric measurements, using a laser spot as a moveable heat source, have revealed local information about thermoelectric response in various materials. This work applies this to examine surprising thermoelectric variation in nominally simple single crystals of gold as well as individual grain boundaries between crystals. Abrupt grain boundaries have little effect on thermoelectric response. Instead, the Seebeck response correlates with crystallographic defects and strain associated with misorientation within the single crystals, detected via electron backscatter diffraction. Annealing reduces these thermoelectric signatures, presumably via relaxation of lattice distortions. These measurements show that minor structural defects in otherwise single-crystalline materials can have readily detectable thermoelectric consequences, a result with implications for many devices and material systems.
Genome-wide variation and transcriptional changes in diverse developmental processes underlie the rapid evolution of seasonal adaptation
Authors: Dowle Edwina J. , Powell Thomas H. Q. , Doellman Meredith M. , Meyers Peter J. , Calvert McCall B. , Walden Kimberly K. O. , Robertson Hugh M. , Berlocher Stewart H. , Feder Jeffrey L. , Hahn Daniel A. , Ragland Gregory J.
Published: September 2020

Significance

Organisms living in seasonal environments must synchronize their growth and reproduction to favorable times of the year. Our study highlights how the timing of dormancy can rapidly evolve to synchronize insects with changes in seasonal food sources. Dormancy is often conceptualized as suspended animation or arrested development, but our results suggest slow, progressive development during dormancy, with the rate of dormancy affected by many genes. Moreover, a population that recently shifted to a food source available earlier in the year has rapidly evolved through changes in many of those same genes. This shows how complex genetics can facilitate adaptation while also leveraging a rapid shift in phenology to understand developmental regulation of dormancy, a fundamental life-history trait in seasonal environments.
CO
2
reduction driven by a pH gradient
Authors: Hudson Reuben , de Graaf Ruvan , Strandoo Rodin Mari , Ohno Aya , Lane Nick , McGlynn Shawn E. , Yamada Yoichi M. A. , Nakamura Ryuhei , Barge Laura M. , Braun Dieter , Sojo Victor
Published: September 2020

Significance

Biology is built of organic molecules, which originate primarily from the reduction of CO
2
through several carbon-fixation pathways. Only one of these—the Wood–Ljungdahl acetyl-CoA pathway—is energetically profitable overall and present in both Archaea and Bacteria, making it relevant to studies of the origin of life. We used geologically pertinent, life-like microfluidic pH gradients across freshly deposited Fe(Ni)S precipitates to demonstrate the first step of this pathway: the otherwise unfavorable production of formate (HCOO
–
) from CO
2
and H
2
. By separating CO
2
and H
2
into acidic and alkaline conditions—as they would have been in early-Earth alkaline hydrothermal vents—we demonstrate a mild indirect electrochemical mechanism of pH-driven carbon fixation relevant to life’s emergence, industry, and environmental chemistry.
Chondrules reveal large-scale outward transport of inner Solar System materials in the protoplanetary disk
Authors: Williams Curtis D. , Sanborn Matthew E. , Defouilloy Céline , Yin Qing-Zhu , Kita Noriko T. , Ebel Denton S. , Yamakawa Akane , Yamashita Katsuyuki
Published: September 2020

Significance

We present a coordinated petrologic, mineral chemistry, and multi-isotopic investigation of individual chondrules to further elucidate the origins and formation histories of planetary materials. We show chondrules from certain meteorites that accreted in the outer Solar System contain an assortment of both inner and outer Solar System material, as well as previously unidentified material. The outward transport of inner Solar System material places important constraints on dynamical models, as outward transport in the disk was thought possible only if significant barriers (e.g., Jupiter) to radial transport of materials do not exist. We show this “barrier” is either not completely impermeable to transport of millimeter-sized materials or additional mechanisms are required to transport materials to the outer Solar System.
El Niño resilience farming on the north coast of Peru
Authors: Caramanica Ari , Huaman Mesia Luis , Morales Claudia R. , Huckleberry Gary , Castillo B. Luis Jaime , Quilter Jeffrey
Published: September 2020

Significance

Disaster management policies are aimed at system resistance: Maintaining or quickly returning to operations established during normal periods. The Peruvian approach to El Niño follows this model, but the cost of reconstruction rises with each event. Meanwhile, archaeological evidence demonstrates that El Niño events were successfully managed by prehispanic farmers, who developed resilient hybrid canal systems that utilized both river water and floodwater for agricultural production. Ancient farmers treated the El Niño phenomenon as part of the norm, and likewise accounted for floodwaters in their irrigation technology. This study calls for a conceptual shift as effective disaster management policy is developed in the context of the global climate crisis.
Targeting myostatin/activin A protects against skeletal muscle and bone loss during spaceflight
Authors: Lee Se-Jin , Lehar Adam , Meir Jessica U. , Koch Christina , Morgan Andrew , Warren Lara E. , Rydzik Renata , Youngstrom Daniel W. , Chandok Harshpreet , George Joshy , Gogain Joseph , Michaud Michael , Stoklasek Thomas A. , Liu Yewei , Germain-Lee Emily L.
Published: September 2020

Significance

Among the major health challenges for astronauts during prolonged space travel are loss of muscle mass and loss of bone mass. Here, we investigated the effects of targeting the signaling pathway mediated by the secreted signaling molecules, myostatin and activin A, in mice sent to the International Space Station. We show that targeting this signaling pathway has significant beneficial effects in protecting against both muscle and bone loss in microgravity, suggesting that this strategy may be effective in preventing or treating muscle and bone loss not only in astronauts on prolonged missions but also in people with disuse atrophy on Earth, such as in older adults or in individuals who are bedridden or wheelchair-bound from illness.
Online processing and offline judgments of L2-English articles
Authors: Cho Jacee
Published: September 2020

This study examines L1-Korean speakers’ online processing and offline judgments of L2-English articles using a self-paced
task (SPRT) targeting implicit knowledge and an untimed acceptability judgment task (AJT) assessing explicit knowledge. SPRT results
indicate that L1-Korean speakers exhibited targetlike online sensitivity to (in)appropriate use of articles, which provides evidence against
the claim that L2-specific morphosyntactic structures cannot be utilized during online comprehension (Jiang, 2007). However, the same L2 speakers showed non-targetlike judgment patterns in the AJT. The discrepancy between online and
offline performance is discussed in terms of the role of task effects on L2 performance and the development of implicit and explicit
knowledge for L2 articles in the acquisition process. Methodological considerations for evaluating L2 knowledge are also discussed.
Multidimensionality, dynamicity, and complexity
Authors: Jiang Na , Wei Xiangqing
Published: September 2020

With the cognitive shift since the 1990s, metaphorical terms have become a recurrent theme in terminological studies. However, how they actually function in science communication has not been fully explored. The issue becomes more pressing today since the exponential expansion of knowledge has heightened our awareness of the need for new designations. And the metaphorical approach is often an economic choice. To gain more insights into the mechanism of metaphorical terms, the authors of the present study will reexamine their functional peculiarities by looking at their linguistic, cognitive and communicative facets respectively. The multidimensional functions of metaphorical terms as exemplified by those in economics are described in detail. More importantly, their dynamic functional potentialities as well as the interplay among them are further discussed.
Methodology for the standardization of terminological resources
Authors: Vezzani Federica , Di Nunzio Giorgio Maria
Published: September 2020

Terminology standardization reflects two different aspects involving the meaning of terms and the structure of
terminological resources. In this paper, we focus on the structural aspect of standardization and we present the work of re-modeling TriMED,
a multilingual terminological database conceived to support multi-register medical communication. In particular, we provide a general
methodology to make the termbase compliant to three of the most recent ISO/TC 37 standards. We focus on the definition of (i) the structural
meta-model of the resource, (ii) the provided data categories and its Data Category Repository, and (iii) the TBX format for its
implementation. In particular, we provide a general methodology to make the termbase compliant to three of the most recent ISO/TC 37
standards. We focus on the definition of (i) the structural meta-model of the resource, (ii) the provided data categories and its Data
Category Repository, and (iii) the TBX format for its implementation.
Uniqueness to inverse acoustic scattering from coated polygonal obstacles with a single incoming wave
Authors: Hu Guang-Hui , Vashisth Manmohan
Published: September 2020

It is proved that a connected polygonal obstacle coated by thin layers together with its surface impedance function can be determined uniquely from the far field pattern of a single incident plane wave. As a by-product, we prove that the wave field cannot be real-analytic on each corner point lying on the convex hull of the scatterer. Our arguments are based on the Schwarz reflection principle for the Helmholtz equation satisfying the impedance boundary condition on a flat boundary.
Multi-synchrosqueezing S-transform for fault diagnosis in rolling bearings
Authors: Zheng Xiaoxia , Wei Yanbin , Liu Jing , Jiang Haisheng
Published: September 2020

Rolling bearings are one of the most significant components of much large machinery, and also one of the components prone to failure. Advanced time–frequency analysis (TFA) methods can provide time–frequency (TF) graphs with more significant features that are critical for fault diagnosis of rolling bearings. In this paper, we propose a new TF algorithm, called the multi-synchrosqueezing S-transform, in which an S-transform is embedded into a multi-synchrosqueezing framework, by reassigning the TF coefficients of the S-transform result in frequency multiple times to achieve the ideal TFA. Using the Rényi entropies to measure the resolution of the TFA and determine iteration, this method can get a better time–frequency representation (TFR) with fewer iterations. The results show that the algorithm can produce TFRs with higher TFR resolution while inheriting the advantages of the S-transform. Through simulation signals and field signals, the effectiveness of the method is verified.
Bimetallic Ag–Au alloy nanocubes for SERS based sensitive detection of explosive molecules
Authors: Kumar Govind , Soni R K
Published: September 2020

We have fabricated Ag–Au alloy nanocubes using the galvanic replacement of silver nanocubes by aqueous HAuCl4 and investigated their morphological, structural, compositional and optical properties. The inter-diffusion between silver and gold at 100 °C leads to the formation of Ag–Au alloy nanocubes with hollow interiors. A broad tuning of the surface plasmon resonance (SPR) wavelength from 624 nm to 920 nm is obtained with the varying volume of HAuCl4. When excited at wavelength 785 nm, the bimetallic Ag–Au nanocubes with pinholes exhibit two-fold Raman intensity enhancement compared to pristine Ag nanocubes. The surface-enhanced Raman spectroscopy (SERS) substrate prepared with Ag–Au alloy nanocubes shows high-intensity enhancement factor of 1.9 × 107 for 11.2 wt% Au content. The SERS-active Ag–Au alloy nanocubes substrates were exploited for the detection of two explosive molecules; p-nitrobenzoic acid (PNBA) and picric acid (PA). Remarkable detection sensitivity and ultra-low detection limit of 1.7 × 10–14 M for PNBA and 4.1 × 10–11 M for PA were obtained, demonstrating the very high SERS detection capabilities of the as-prepared substrate.
AC loss measurement and simulation in a REBCO coil assembly utilising low-loss magnetic flux diverters
Authors: You Shuangrong , Staines Mike , Sidorov Gennady , Miyagi Daisuke , Badcock Rodney A , Long Nicholas J , Jiang Zhenan
Published: September 2020

AC loss in high temperature superconducting (HTS) coils affects the performance of HTS devices. Using magnetic flux diverters (MFDs) is an effective way to reduce AC loss in HTS coils. In this paper, measurement and finite element method simulation of AC loss results in a REBCO coil assembly comprising four double pancake coils with two molypermalloy-powder MFDs are presented. Both experimental and numerical results show that MFDs can significantly reduce the AC loss in the REBCO coil assembly while generating negligible loss in themselves. Further, the influence of the distance between the coil assembly and the diverters on AC loss reduction is explored. Compared with the AC loss data in the coil assembly without MFDs, over 80% AC loss reduction is achieved when the distance between the coil assembly and the diverters is at its minimum value, 2 mm. The simulation results reveal that the AC loss reduction in the coil assembly is mainly due to the reduction of the radial (perpendicular) magnetic field component to the surface of REBCO wires in the end windings of the coil assembly.
Diagnosing fast ion redistribution due to sawtooth instabilities using fast ion deuterium-α spectroscopy in the mega amp spherical tokamak
Authors: Jackson A.R. , Jacobsen A.S. , McClements K.G. , Michael C.A. , Cecconello M.
Published: September 2020

A comparison between fast ion measurements and sawtooth models in the Mega Amp Spherical Tokamak (MAST) is extended to include fast ion deuterium-alpha (FIDA) data. It is concluded that FIDA data cannot be used to distinguish between three alternative models used in the plasma transport/fast particle code TRANSP/NUBEAM to simulate fast ion redistribution during sawteeth. For FIDA lines-of-sight that probe the sawtoothing region, at each sawtooth crash there is an overall drop in the emission of up to 60%. Data from passive FIDA lines-of-sight (i.e. with emission resulting from neutralisation by thermal neutrals in the plasma periphery rather than beam neutrals) show a sudden increase in the emission following sawtooth crashes. The subsequent decay in the emission in these passive channels indicates that redistributed passing fast ions are rapidly lost from the edge region, probably as a result of charge-exchange reactions with edge neutrals.
Ecological status of river networks: stream order-dependent impacts of agricultural and urban pressures across ecoregions
Authors: Büttner Olaf , Jawitz James W , Borchardt Dietrich
Published: September 2020

Why have ecological targets for the majority of water bodies in Europe not been met despite decades of water protection programs? We hypothesize that restoration strategies have not adequately accounted for whole-river network perspectives, including interactions between stream orders, spatial patterns of pollutant sources, and ecoregion-dependent susceptibility. We used high-resolution data from Germany to identify relationships between urban wastewater-river discharge fraction (UDF), agricultural land use fraction (ALF), and ecological status by stream order across three ecoregions. Low-flow UDF values were used to reflect the strong vulnerability of low-order streams under these conditions. We found ecological status of good or better in less than 8% of all river sections with the highest proportions in low-order streams and complete disappearance at higher orders. Increasing ALF impaired the ecological status for river reaches across all stream orders. In contrast, relationships between UDF and ecological status impairment were significant only in low-order streams, independent from ecoregion. Concentrating integrative restoration efforts in low-order streams would maximize the potential to mitigate anthropogenic impacts.
The Beginning of the End
Authors: Khoshpouri Parisa , Bahar Rayeheh , Khoshpouri Pegah , Ebrahimi Amitis , Ghahramani Omid , Singh Sekhon Amardeep , Mansouri Somayeh , Choo-Foo Jade , Khosa Faisal
Published: September 2020

Objectives

The purpose of this study was to determine the relationship between gender, research productivity, academic rank, and departmental leadership positions of pathology faculty in North America.

Methods

The online information presented for the faculty members in all American- and Canadian-accredited pathology residency programs’ official websites and Elsevier’s SCOPUS were queried to assess research productivity, academic ranks, and leadership positions.

Results

Among 5,228 academic pathologists included in our study, there were 3,122 (59.7%) males and 2,106 (40.3%) females. Male faculty held higher academic ranks (being professor) and leadership positions (chair/program director) (P < .0001). Males were more likely to hold combined MD-PhD degrees (P < .0001) than females. The median h-index for the male faculty was 17 vs 9 for the female faculty (P = .023).

Conclusions

Gender has a significant influence on leadership positions, academic ranks, and research productivity among pathology faculty members in North America.
Disulfiram Ethanol Reaction with Alcohol-Based Hand Sanitizer: An Exploratory Study
Authors: Ghosh Abhishek , Mahintamani Tathagata , Balhara Y P S , Roub Fazl E , Basu Debashish , BN Subodh , Mattoo S K , Mishra Eepsita , Sharma Babita
Published: September 2020

Aims

We conducted a cross-sectional survey to estimate the prevalence and clinical manifestation of disulfiram ethanol reaction (DER) and isopropanol toxicity (IT) in patients with alcohol use disorders, on disulfiram. Alcohol-based hand rub contains either ethanol or isopropanol or both. COVID-19 pandemic has led to wide scale usage of sanitizers. Patients with alcohol use disorders, on disulfiram, might experience disulfiram ethanol like reactions with alcohol-based sanitizers.

Methods

We telephonically contacted 339 patients, prescribed disulfiram between January 2014 and March 2020. The assessment pertained to the last 3 months (i.e. third week of March to third week of June 2020).

Result

The sample consisted of middle-aged men with a mean 16 years of alcohol dependence. Among the 82 (24%) patients adherent to disulfiram, 42 (12.3%) were using alcohol-based hand rubs. Out of these, a total of eight patients (19%; 95% CI 9–33) had features suggestive of DER; four of whom also had features indicative of IT. Five patients (62.5%) had mild and self-limiting symptoms. Severe systemic reactions were experienced by three (37.5%). Severe reactions were observed with exposure to sanitizers in greater amounts, on moist skin or through inhalation.

Conclusion

Patients on disulfiram should be advised to use alternate methods of hand hygiene.
The night out task and scoring application: an ill-structured, open-ended clinic-based test representing cognitive capacities used in everyday situations
Authors: Schmitter-Edgecombe Maureen , Cunningham Reanne , McAlister Courtney , Arrotta Kayela , Weakley Alyssa
Published: September 2020

Objective

The night out task (NOT) was developed as a naturalistic, open-ended, multitasking measure that requires individuals to complete eight subtasks comparable to those encountered during real-world functioning (e.g., pack travel bag, prepare tea). We examined psychometric properties and administration feasibility of this direct observation measure within a clinic-like setting using a tablet-based coding application.

Method

A sample of 148 community-dwelling older adults (82% cognitively healthy; 18% mild cognitive impairment) and 57 younger adults completed the NOT along with other neurocognitive tests and questionnaires.

Results

Inter-rater reliability across NOT primary (i.e., time, accuracy, efficiency) and process-related (e.g., error-types, self-corrections) variables was mostly excellent. NOT primary measures showed expected patterns of convergent and discriminant validity with measures of cognition, demographics, and well-being. External validity was established by the NOT ability to distinguish between age and diagnostic (cognitively healthy vs. mild cognitive impairment) groups. Demonstrating incremental validity, the NOT primary variables (execution time in particular) were predictive of self-reported functional abilities and completion quality of in-home everyday tasks over and earlier variables such as demographics, cognition, and mobility.

Conclusions

These findings suggest that the NOT and its app interface, which allows for continuous logging of observations, are a feasible in-clinic measure to assess cognitive capacities important for real-world functioning. With further validation, the NOT may allow for earlier detection of functional difficulties. Understanding errors and strategies used during NOT performance could also have implications for individualized interventions.
VPTMdb: a viral posttranslational modification database
Authors: Xiang Yujia , Zou Quan , Zhao Lilin
Published: September 2020

In viruses, posttranslational modifications (PTMs) are essential for their life cycle. Recognizing viral PTMs is very important for a better understanding of the mechanism of viral infections and finding potential drug targets. However, few studies have investigated the roles of viral PTMs in virus–human interactions using comprehensive viral PTM datasets. To fill this gap, we developed the first comprehensive viral posttranslational modification database (VPTMdb) for collecting systematic information of PTMs in human viruses and infected host cells. The VPTMdb contains 1240 unique viral PTM sites with 8 modification types from 43 viruses (818 experimentally verified PTM sites manually extracted from 150 publications and 422 PTMs extracted from SwissProt) as well as 13 650 infected cells’ PTMs extracted from seven global proteomics experiments in six human viruses. The investigation of viral PTM sequences motifs showed that most viral PTMs have the consensus motifs with human proteins in phosphorylation and five cellular kinase families phosphorylate more than 10 viral species. The analysis of protein disordered regions presented that more than 50% glycosylation sites of double-strand DNA viruses are in the disordered regions, whereas single-strand RNA and retroviruses prefer ordered regions. Domain–domain interaction analysis indicating potential roles of viral PTMs play in infections. The findings should make an important contribution to the field of virus–human interaction. Moreover, we created a novel sequence-based classifier named VPTMpre to help users predict viral protein phosphorylation sites. VPTMdb online web server (http://vptmdb.com:8787/VPTMdb/) was implemented for users to download viral PTM data and predict phosphorylation sites of interest.
Machine learning application identifies novel gene signatures from transcriptomic data of spontaneous canine hemangiosarcoma
Authors: Cheng Nuojin , Schulte Ashley J , Santosa Fadil , Kim Jong Hyuk
Published: September 2020

Angiosarcomas are soft-tissue sarcomas that form malignant vascular tissues. Angiosarcomas are very rare, and due to their aggressive behavior and high metastatic propensity, they have poor clinical outcomes. Hemangiosarcomas commonly occur in domestic dogs, and share pathological and clinical features with human angiosarcomas. Typical pathognomonic features of this tumor are irregular vascular channels that are filled with blood and are lined by a mixture of malignant and nonmalignant endothelial cells. The current gold standard is the histological diagnosis of angiosarcoma; however, microscopic evaluation may be complicated, particularly when tumor cells are undetectable due to the presence of excessive amounts of nontumor cells or when tissue specimens have insufficient tumor content. In this study, we implemented machine learning applications from next-generation transcriptomic data of canine hemangiosarcoma tumor samples (n = 76) and nonmalignant tissues (n = 10) to evaluate their training performance for diagnostic utility. The 10-fold cross-validation test and multiple feature selection methods were applied. We found that extra trees and random forest learning models were the best classifiers for hemangiosarcoma in our testing datasets. We also identified novel gene signatures using the mutual information and Monte Carlo feature selection method. The extra trees model revealed high classification accuracy for hemangiosarcoma in validation sets. We demonstrate that high-throughput sequencing data of canine hemangiosarcoma are trainable for machine learning applications. Furthermore, our approach enables us to identify novel gene signatures as reliable determinants of hemangiosarcoma, providing significant insights into the development of potential applications for this vascular malignancy.
svMIL: predicting the pathogenic effect of TAD boundary-disrupting somatic structural variants through multiple instance learning
Authors: Nieboer Marleen M. , de Ridder Jeroen
Published: September 2020

Motivation

Despite the fact that structural variants (SVs) play an important role in cancer, methods to predict their effect, especially for SVs in non-coding regions, are lacking, leaving them often overlooked in the clinic. Non-coding SVs may disrupt the boundaries of Topologically Associated Domains (TADs), thereby affecting interactions between genes and regulatory elements such as enhancers. However, it is not known when such alterations are pathogenic. Although machine learning techniques are a promising solution to answer this question, representing the large number of interactions that an SV can disrupt in a single feature matrix is not trivial.

Results

We introduce svMIL: a method to predict pathogenic TAD boundary-disrupting SV effects based on multiple instance learning, which circumvents the need for a traditional feature matrix by grouping SVs into bags that can contain any number of disruptions. We demonstrate that svMIL can predict SV pathogenicity, measured through same-sample gene expression aberration, for various cancer types. In addition, our approach reveals that somatic pathogenic SVs alter different regulatory interactions than somatic non-pathogenic SVs and germline SVs.

Availability and implementation

All code for svMIL is publicly available on GitHub: https://github.com/UMCUGenetics/svMIL.

Supplementary information

Supplementary data are available at Bioinformatics online.
FastSK: fast sequence analysis with gapped string kernels
Authors: Blakely Derrick , Collins Eamon , Singh Ritambhara , Norton Andrew , Lanchantin Jack , Qi Yanjun
Published: September 2020

Motivation

Gapped k-mer kernels with support vector machines (gkm-SVMs) have achieved strong predictive performance on regulatory DNA sequences on modestly sized training sets. However, existing gkm-SVM algorithms suffer from slow kernel computation time, as they depend exponentially on the sub-sequence feature length, number of mismatch positions, and the task’s alphabet size.

Results

In this work, we introduce a fast and scalable algorithm for calculating gapped k-mer string kernels. Our method, named FastSK, uses a simplified kernel formulation that decomposes the kernel calculation into a set of independent counting operations over the possible mismatch positions. This simplified decomposition allows us to devise a fast Monte Carlo approximation that rapidly converges. FastSK can scale to much greater feature lengths, allows us to consider more mismatches, and is performant on a variety of sequence analysis tasks. On multiple DNA transcription factor binding site prediction datasets, FastSK consistently matches or outperforms the state-of-the-art gkmSVM-2.0 algorithms in area under the ROC curve, while achieving average speedups in kernel computation of ∼100× and speedups of ∼800× for large feature lengths. We further show that FastSK outperforms character-level recurrent and convolutional neural networks while achieving low variance. We then extend FastSK to 7 English-language medical named entity recognition datasets and 10 protein remote homology detection datasets. FastSK consistently matches or outperforms these baselines.

Availability and implementation

Our algorithm is available as a Python package and as C++ source code at https://github.com/QData/FastSK

Supplementary information

Supplementary data are available at Bioinformatics online.