bluuebunny/crossref_metadata_2025 huggingface dataset:
Ramularia geranii
.
Authors: Andrianova T. V. , Minter D. W.
Published: August 2022

A description is provided for
Ramularia geranii
, which seems to be parasitic, with records on living leaves of
Geranium
and other plant species, sometimes causing leaf spot symptoms, particularly on their lower sides. It has also been observed on dead fallen leaves. Some information on its associated organisms and substrata, habitats, dispersal and transmission, and conservation status is given, along with details of its geographical distribution (Africa (Morocco, South Africa), North America (USA (Alaska, California, Florida, Idaho, Kansas, Louisiana, Maryland, Massachusetts, Ohio, Oregon, Washington, Wyoming)), South America (Argentina), Asia (Armenia, Azerbaijan, Georgia, Iran, Japan, Kazakhstan (Aktobe oblast, former Almaty oblast, Karaganda oblast, former Kokchetavskaya oblast, Pavlodar oblast, former Taldy-Kurgan oblast, Zhambyl oblast), Kyrgyzstan, Mongolia, Russia (Amur oblast, Khabarovsk krai, Krasnoyarsk krai, Novosibirsk oblast, Primorsky krai, Tyumen' oblast), Tajikistan, Turkey, Uzbekistan), Atlantic Ocean (Portugal (Azores), Spain (Canary Islands)), Europe (Andorra, Austria, Belgium, Bulgaria, Czech Republic, Denmark, Estonia, Finland, France, Germany, Greece, Hungary, Iceland, Ireland, Italy, Latvia, Lithuania, Montenegro, Netherlands, Norway, Poland, Portugal, Romania, Russia (Belgorod oblast, Kirov oblast, Kursk oblast, Leningrad oblast, Lipetsk oblast, Nizhny Novrogod oblast, Penza oblast, Pskov oblast, Republic of Bashkortostan, Republic of Kabardino-Balkaria, Republic of Karelia, Ryazan' oblast, Saratov oblast, Smolensk oblast, Tambov oblast, Ulyanovsk oblast, Voronezh oblast, Yaroslavl' oblast), Serbia, Slovakia, Spain, Sweden, Switzerland, Ukraine, UK)). No evaluation has been made of any possible positive economic impact of this fungus and no reports of negative economic impacts have been found.
Rhizocarpon oederi
. [Descriptions of Fungi and Bacteria].
Authors: Minter D. W. , Cannon P. F.
Published: August 2022

A description is provided for
Rhizocarpon oederi
, found on rocks. Some information on its associated organisms and substrata, dispersal and transmission, habitats and conservation status is given, along with details of its geographical distribution (Antarctica (South Georgia), Arctic Ocean (Greenland, Norway, Svalbard and Jan Mayen), Asia (Japan, Kazakhstan, Russia, Turkey), Europe (Austria, Belgium, Czech Republic, Denmark, Estonia, Finland, France, Germany, Iceland, Ireland, Isle of Man, Italy, Kosovo, Netherlands, Norway, Poland, Portugal, Russia, Slovakia, Spain, Sweden, Switzerland, UK), North America (Canada, British Columbia, New Brunswick, Newfoundland and Labrador, Nunavut, Ontario, Quebec, USA, Alabama, Alaska, Maine, Michigan, Minnesota, New Hampshire, New York, North Carolina, Tennessee, Washington, Wisconsin), South America (Argentina)).
Apple necrotic mosaic virus. [Distribution map].
Authors: CABI  , EPPO
Published: August 2022

A new distribution map is provided for Apple necrotic mosaic virus. Martellivirales: Bromoviridae: Ilarvirus. Host: apple (
Malus domestica
). Information is given on the geographical distribution in Asia (China, Beijing, Gansu, Guizhou, Hebei, Jilin, Liaoning, Shaanxi, Shandong, Shanxi, Sichuan, Xinjiang, Yunnan, India, Jammu and Kashmir, Japan, Korea Republic).
Xanthomonas axonopodis
pv.
begoniae
. [Distribution map].
Authors: CABI  , EPPO
Published: August 2022

A new distribution map is provided for
Xanthomonas axonopodis
pv.
begoniae
(Takimoto) Vauterin et al. Gammaproteobacteria: Lysobacterales: Lysobacteraceae. Host:
Begonia
spp. Information is given on the geographical distribution in Africa (Mauritius), Asia (China, Iran, Japan, Taiwan, Turkey), Europe (Belgium, Czechia, Denmark, France, Germany, Hungary, Netherlands, Norway, United Kingdom), North America (Canada, Saint Vincent and the Grenadines, United States, Hawaii, Massachusetts, Michigan, Mississippi, Montana, New York, Oregon, Pennsylvania, South Carolina), Oceania (Australia, New South Wales, South Australia, Western Australia, New Zealand), South America (Argentina, Brazil).
Spectral broadening of femtosecond pulses during SRS in hydrogen
Authors: Losev L L
Published: August 2022

It was shown that the spectral broadening of femtosecond laser pulses during stimulated Raman scattering (SRS) in hydrogen is determined by two nonlinear processes leading to phase modulation of the laser wave. Namely, the dependence of the refractive index of the gas on the intensity of laser radiation and the dependence of the refractive index on the ratio of the number of molecules at the ground and first vibrational levels of the hydrogen molecule, which changes during SRS.
Automated deep brain stimulation programming with safety constraints for tremor suppression in patients with Parkinson’s disease and essential tremor
Authors: Sarikhani Parisa , Ferleger Benjamin , Mitchell Kyle , Ostrem Jill , Herron Jeffrey , Mahmoudi Babak , Miocinovic Svjetlana
Published: August 2022

Objective. Deep brain stimulation (DBS) programming for movement disorders requires systematic fine tuning of stimulation parameters to ameliorate tremor and other symptoms while avoiding side effects. DBS programming can be a time-consuming process and requires clinical expertise to assess response to DBS to optimize therapy for each patient. In this study, we describe and evaluate an automated, closed-loop, and patient-specific framework for DBS programming that measures tremor using a smartwatch and automatically changes DBS parameters based on the recommendations from a closed-loop optimization algorithm thus eliminating the need for an expert clinician. Approach. Bayesian optimization which is a sample-efficient global optimization method was used as the core of this DBS programming framework to adaptively learn each patient’s response to DBS and suggest the next best settings to be evaluated. Input from a clinician was used initially to define a maximum safe amplitude, but we also implemented ‘safe Bayesian optimization’ to automatically discover tolerable exploration boundaries. Main results. We tested the system in 15 patients (nine with Parkinson’s disease and six with essential tremor). Tremor suppression at best automated settings was statistically comparable to previously established clinical settings. The optimization algorithm converged after testing

15.1
±
0.7

settings when maximum safe exploration boundaries were predefined, and

17.7
±
4.9

when the algorithm itself determined safe exploration boundaries. Significance. We demonstrate that fully automated DBS programming framework for treatment of tremor is efficient and safe while providing outcomes comparable to that achieved by expert clinicians.
Influence of the number of trials on evoked motor cortical activity in EEG recordings
Authors: Borràs Marta , Romero Sergio , Alonso Joan F , Bachiller Alejandro , Serna Leidy Y , Migliorelli Carolina , Mañanas Miguel A
Published: August 2022

Objective. Improvements in electroencephalography enable the study of the localization of active brain regions during motor tasks. Movement-related cortical potentials (MRCPs), and event-related desynchronization (ERD) and synchronization are the main motor-related cortical phenomena/neural correlates observed when a movement is elicited. When assessing neurological diseases, averaging techniques are commonly applied to characterize motor related processes better. In this case, a large number of trials is required to obtain a motor potential that is representative enough of the subject’s condition. This study aimed to assess the effect of a limited number of trials on motor-related activity corresponding to different upper limb movements (elbow flexion/extension, pronation/supination and hand open/close). Approach. An open dataset consisting on 15 healthy subjects was used for the analysis. A Monte Carlo simulation approach was applied to analyse, in a robust way, different typical time- and frequency-domain features, topography, and low-resolution electromagnetic tomography. Main results. Grand average potentials, and topographic and tomographic maps showed few differences when using fewer trials, but shifts in the localization of motor-related activity were found for several individuals. MRCP and beta ERD features were more robust to a limited number of trials, yielding differences lower than 20% for cases with 50 trials or more. Strong correlations between features were obtained for subsets above 50 trials. However, the inter-subject variability increased as the number of trials decreased. The elbow flexion/extension movement showed a more robust performance for a limited number of trials, both in population and in individual-based analysis. Significance. Our findings suggested that 50 trials can be an appropriate number to obtain stable motor-related features in terms of differences in the averaged motor features, correlation, and changes in topography and tomography.
Containerized immutable maritime data sharing utilizing Distributed Ledger Technologies
Authors: Knutsen Knut Erik , Liang Qin , Karandikar Nikita , Ibrahim Imran Halimi Bin , Tong Xiao Gang Tony , Tam Jacob Jun Hui
Published: August 2022

In recent years, distributed ledger technologies (DLTs), especially blockchain technology, has become a popular topic and is being implemented in different industries. Ships are expected to be equipped with more advanced equipment and less crew onboard. The communication and information sharing between different maritime stakeholders such as business partners, port authorities, tax authorities, class societies, flag states, IMO and EU become more important than ever. Trust and authenticity are key properties when utilizing data for safety or business critical applications, and will only increase in importance as automation levels increase towards fully autonomous ships and trading systems. The implementation of DLTs as close as possible to the data source helps provide a reliable, trustworthy way to share, process and verify the data. The objective of this paper is to explore how tamperfree maritime data sharing can enable automated transactions between vessels and shore-based entities. Singapores TradeTrust platform has shown that digitalization of international trade has great potential. In this paper we explore how further enhancements may be implemented and how the distributed ledger VeChain, as compared to Ethereum, have some distinct advantages that may be beneficial for continued automation and efficiency gains. The electronic Bill of Lading was taken as an example to demonstrate the concept. Reporting requirements from the other maritime data sharing scenarios are also expected to require a way of ensuring tamperfree data.
Exploring navigator roles and tasks in transitioning towards supervisory control of autonomous collision avoidance systems
Authors: van de Merwe G K , Mallam S C , Engelhardtsen Ø , Nazir S
Published: August 2022

This study aims to systematically map and assess performance requirements for collision avoidance manoeuvring for two cases. A case where the navigator performs collision avoidance, and a case where collision avoidance is performed by collision avoidance system where the navigator acts as its supervisor. An appraisal of collision avoidance manoeuvring was performed based on three data sources: the collision avoidance regulations, a ferry operator’s procedures, and interviews with navigators including in situ observations. A framework was established in which the gathered data was structured and analysed using a cognitive task analysis approach. Based on the results, performance requirements and information needs were established. Further work will focus on detailing the navigator’s information needs and the corresponding system’s transparency requirements to support effective human performance.
Evaluation of effectiveness of the STAMP / STPA in risk analysis of autonomous ship systems
Authors: Yamada Tomoaki , Sato Makoto , Kuranobu Rikiya , Watanabe Ryo , Itoh Hiroko , Shiokari Megumi , Yuzui Tomohiro
Published: August 2022

To ensure safety of Maritime Autonomous Surface Ships (MASS), the importance of risk assessment is emphasized in classification societies, but the assessment method is not specified, and standardization of the method is expected. In the risk analysis of conventional ship, we focus on equipment failure mainly on hardware, but in MASS, it is necessary to analyze not only hardware but also large-scale and complicated systems including software and human beings. STAMP / STPA is an analysis method for large-scale and complicated systems, and it may be applicable to MASS risk analysis. In this paper, we will verify the effectiveness of STAMP / STPA in the initial stage of MASS design and consider it from a certification point of view.
Prediction of tidal-driven currents using convolutional neural network
Authors: Choo Jian Feng , Chow Jeng Hei , Tkalich Pavel
Published: August 2022

Efficient forecasting models of coastal currents are required for the predictive control of smart vessels with autonomous or remote operating capabilities. Accurate physics-based numerical models demand computational resources that often are unavailable onboard ships; moreover, internet bandwidth at remote locations might not be sufficient to exchange the large computational files with onshore servers. In this case, light and efficient Data-Driven Models (DDM) may be developed to be used as a surrogate for a physics-based model.

Currents and surface elevation are hydrodynamic variables driven by astronomic tide potential, allowing for harmonic analysis and synthesis of otherwise irregular solutions of Navier-Stokes equations. Once numerical solutions are obtained and analysed in the Fourier domain, the identified harmonics (tide constituents) can be used as a dataset to train the DDM. One approach to building a DDM is by utilizing a Convolutional Neural Network (CNN).

CNN is mainly applied in image recognition processes, where it learns the spatial features of image matrices of pixels arranged in columns and rows and uses the learned features to predict an output. This approach can be applied to 2D or 3D fields of predominantly tidal-driven coastal currents. This paper extends the CNN framework to approximate and predict coastal hydrodynamic state variables in space and time. The depth-averaged Navier-Stokes equations were used to create the dataset necessary to train the adopted CNN autoencoder architecture.

Two methods of CNN model development are explored. The first method assesses CNN’s capabilities for time forward prediction, using 2D time series of hydrodynamic variables. The second method investigates CNN’s parameter (using Manning number) prediction ability using 2D spatial plots formed by the top 20 most energetic tidal constituents that were obtained from the numerical solution. The hyperparameters of the CNN model for both methods were carefully optimized and tuned using the loss function, Root Mean Square Error (RMSE). The coefficient of determination, the relative error of the time series, and its amplitude and phase were used to gauge the performance of the CNN model for both methods at the final testing stage.

Once accurate solutions are achieved, the trained DDM is almost instantaneous and uses negligible computational resources as compared to traditional fluid solvers. Therefore, trained DDM can be deployed onboard ships where global forecast information (e.g., from Global Forecast System) can be used to provide an accurate prediction of the current forcing. To generate the instantaneous current predictions for navigation and smart ship control, the global data can be pulled or pushed to the ship before the mission.
Maritime Autonomous Surface Ships: Automation Transparency for Nearby Vessels
Authors: Alsos Ole Andreas , Hodne Philip , Skåden Oskar Kristoffer , Porathe Thomas
Published: August 2022

In the future, maritime autonomous surface ships (MASS) will become more advanced, and mariners will move from the bridge to remote operation centres. To avoid dangerous situations and frequent intervention from the operators, a MASS needs to perceive the environment and calculate the current state and future intention of nearby ships. Another challenge for a MASS is to explain the decisions of its algorithms and make the artificial intelligence’s decisions transparent to not only the operators, but also external stakeholders, such as passengers, vessel traffic services, and nearby ships. This is calledautomation transparency. In this paper we focus on how MASS, through various means of maritime communication, can (1)expresstheir own state and intention to other ships and (2)perceiveother ships’ state and intention. Towards that, we first analyse current maritime communication methods in terms of how well they can be expressed and perceived by today’s MASS in comparison to traditional ships. Next, we analyse which gaps in their communication should be focused on to maximise safety at sea. Finally, we present multiple design recommendations for naval architects, human factors engineers, and interaction designers who are designing and building the next generation of MASS.
milliAmpere: An Autonomous Ferry Prototype
Authors: Brekke Edmund F , Eide Egil , Eriksen Bjørn-Olav H , Wilthil Erik F , Breivik Morten , Skjellaug Even , Helgesen Øystein K , Lekkas Anastasios M. , Martinsen Andreas B , Thyri Emil H. , Torben Tobias , Veitch Erik , Alsos Ole A , Johansen Tor Arne
Published: August 2022

In this paper, we summarize the experiences with the autonomous passenger ferry development prototype milliAmpere, which has been used as a test platform in several research projects at the Norwegian University of Science and Technology (NTNU) since 2017. New algorithms for motion planning, motion control, collision avoidance, docking, multi-target tracking and localization have been developed and verified in full-scale experiments with milliAmpere. The infrastructure surrounding milliAmpere includes several sensor rigs supporting research on multi-sensor fusion and situational awareness, and a shore control lab which can be used to study the interaction between human operators and the autonomous ferry. Building upon the experiences with milliAmpere, the full-scale autonomous ferry milliAmpere2 was recently launched.
On the implementation of a rule-based system to perform assessment of COLREGs onboard maritime autonomous surface ships
Authors: Constapel M , Koch P , Burmeister H-C
Published: August 2022

Complying to the Convention on the International Regulations for Preventing Collisions at Sea (COLREGs) is one of the key challenges for Maritime Autonomous Surface Ships (MASS) to perform autonomous navigation. We propose a rule-based approach utilizing operationalized situation statements to assess vessel encounters with regards to COLREGs. The statements contain basic informational pieces to describe the relation between two vessels. For processing with a rule-based inference system, the statements are grouped into rule sets to determine applicable COLREGs rules for an encounter situation. Implementation results are shown in the context of the B ZERO project, outlining how the approach can be utilized onboard a seagoing ship.
Biofuel Adoption Pathways for Cargo Vessels under Carbon Tax
Authors: Xiao Zengqi , Lam Jasmine Siu Lee , Thepsithar Prapisala , Milla Kevin
Published: August 2022

According to the International Maritime Organization (IMO) Greenhouse Gas (GHG) Strategy, the shipping industry by 2050 aims to reduce by at least 50% of GHG emission level in 2008. Among various alternative energy sources, biofuels illustrate potential as a drop-in fuel using existing shipboard technologies, bunkering infrastructure, and a new fuel replacing conventional fossil-based fuels. However, the decision to adopt biofuel in vessels depends on various factors. Biofuels may be derived from different feedstock and production routes and thus demonstrate different economic and environmental performances. The compatible type of engines also differs across biofuels, implying differences in capital cost. In addition, a high carbon tax may push the usage of a more expensive biofuel, while a low carbon tax may not drive the switch from fossil fuel. This study aims to analyse biofuel adoption pathways under carbon tax to achieve a net 50% GHG emission reduction for cargo vessels, including bulk carriers, container vessels and tankers. The study focuses on the following types of fuels: low sulphur fuel oil (LSFO), marine gas oil (MGO), Liquefied natural gas (LNG), biodiesel in the form of palm methyl ester (PME), hydrotreated vegetable oil (HVO), and bio-LNG.
A quick surface heat flux estimation method for typical structures of high-speed aircrafts
Authors: Wu Long , Wang Feng , Wang Qi , Han Yiyu , Li Zhengzhou
Published: August 2022

Surface heat flux estimation of high-speed aircrafts is an inverse problem and high system ill-posedness usually leading to instability and low accuracy. In this study, an efficient method is proposed to solve it stably. The heat flux identification equation is established based on the superposition principle. Tikhonov regularization method with the parameter determined by generalized cross validation is applied to reduce the sensitivity to measurement error. A calibration method is presented to correct the pulse sensitivity coefficient matrix so that the estimation method can be used for complex three-dimensional structures. Numerical studies demonstrate the efficiency and accuracy.
Uncertainty analysis and visualization for a coupled thermohydraulics-neutronics simulation by deterministic sampling
Authors: Yang Wen , Huang Jun , Tian Zhaofei , Chen Guangliang
Published: August 2022

Uncertainty quantification and sensitivity analysis by deterministic sampling is performed on a thermohydraulics-neutronics coupling simulation of a 5×5 rod bundle in pressurized water reactor. Thermohydraulics calculation is conducted by a CFD simulation and neutronics calculation is conducted by method of characteristic (MOC). The coupling simulation of CFD and MOC, together with large number of calculations needed by random sampling in uncertainty quantification, leads to high computational cost. Therefore, deterministic sampling is introduced in this study and proves its efficiency. Moreover, the calculated results usually have some distribution pattern on the selected section, using mass average value as output is unable to reflect the distribution feature. Therefore, a method realized by Python program is introduced to perform uncertainty quantification and sensitivity analysis of the outputs on the outlet section in fine-mesh level. It is found that the uncertainty of outputs and the inputs’ impact on outputs vary in different areas at the outlet section.
Development of a single-scale initial flow field into steady homogeneous turbulence with validating a constructed Fourier spectral analysis
Authors: Suzuki Hiroki , Kouchi Toshinori
Published: August 2022

This study presents the development of a single-scale initial velocity field into steady homogeneous isotropic turbulence. Here, we verify a constructed Fourier spectral analysis, which is then used to approach the present issue. The present homogeneous isotropic turbulence is maintained steady by using a linear forcing scheme of Lundgren (2003). Here, two values of the primary coefficient are set here for this scheme. The initial velocity field is also set to maintain the flow globally isotropic. Temporal developments of turbulence statistics, visualization results and structure functions are examined in this study. As shown in a previous study, Rosales and Meneveau (2005), the turbulence length scale at a steady-state could remain independent of a value used for the linear forcing coefficient. The turbulence fields needed 10 to 15 times longer than the turbulence time scale to achieve this steady-state. A larger amount of time was needed for the structure functions to reach their steady-state profiles than for the turbulence statistics.
Flow structure of pitched and skewed microjet vortex generator array
Authors: Da Xingya , Yi Yuan , Zhang Yue , Guo Longkai , Tao Yang
Published: August 2022

To understand the micro-vortex structure of Microjet Vortex Generators, a plate with pitched and skewed jet holes was established. Simulations using SST-DDES method based on WENO scheme were conducted to analyse the effect of jet pressure, hole interval and incoming boundary layer thickness on the flow structure. The pitch angle and skew angle are 55 degrees and 45 degrees respectively. The total pressure of microjets ranges from 2.5 to 3.5 times the mainstream pressure. The interval of microjets ranges from 6.75 to 13.5 diameters of the hole, and the thickness of incoming boundary layer ranges from 2 to 4 diameters of the hole. The flow field is dominated by three vortices, including a main vortex and two secondary vortices which are significantly influenced by jet pressure and interval. The interaction between secondary vortices and main vortex plays an important role in the process of boundary layer mixing.
Improved theory of the elastic-plastic response of spherical containment vessels subjected to internal blast loading and its application
Authors: He Zeng , Wang Zhihuan , Zhang Baihua , Jia Leiming , Tian Zhou
Published: August 2022

Baker built the displacement equations of motion for a thin spherical shell to spherically symmetric internal blast loading, and further provided the analytical solution of the elastic-plastic response under a triangular decaying pressure, neglecting shell thinning and radius variation [1], which was widely used in the fields of analysis and design of explosion containment vessels. However, it appears that some improvements and corrections are needed when we revisit this classic problem. In this paper, the elastic-plastic response of thin spherical shells is investigated mathematically. The complete equations of motion for three models are developed. Then the main ideas of the analytical and numerical methods are presented, as well as some important procedures and results by using Laplace transform techniques, which are convenient to use and generalize. Three typical examples are solved to exhibit differences between our improved theory and Baker’s [1]. Furthermore, our models are employed to gain some insights into response regularities, including the effect of various degrees of strain-hardening on maximum displacements under impulsive loading, and the effect of loading duration on the shell displacement for a perfectly plastic material.
The dominant mechanism of gold film damage induced by near-threshold femtosecond laser: non-thermal deformation or thermal ablation
Authors: Zhang Ke , Sun Jingya
Published: August 2022

Near-threshold femtosecond laser produces nanostructures on the gold film, which has received much attention in applications. However, the theoretical researches on the early stage of gold film excitation induced by the femtosecond laser are scarce, because of the ultrafast and non-equilibrium characteristics. In this study, stress and temperature distributions in different thicknesses of gold film induced by the near-threshold fluences were calculated. At the fluence below the melting threshold, we found that only the 30 nm gold films might be damaged by the non-thermal deformation. At the fluence of the melting threshold, the dominant damage mechanism shifted from non-thermal deformation to thermal melting as the gold film thickness increased. Our study provided a way to distinguish the dominant damage mechanism of gold film and it was valuable for the theoretical study of near-threshold processing.
Quaternionic Dirac oscillator
Authors: Sadovskií D A , Zhilinskií B I
Published: August 2022

We construct an elementary quaternionic slow–fast Hamiltonian dynamical system with one formal control parameter and two slow degrees of freedom as half-integer spin in resonance 1:1:2 with two slow oscillators. Invariant under spin reversal and having a codimension-5 crossing of its fast Kramers-degenerate semi-quantum eigenvalues, our system is the dynamical equivalent of the spin-quadrupole model by Avron et al (1989 Commun. Math. Phys.
124 595–627), exhibiting non-Abelian geometric phases. The equivalence is uncovered through the equality of the spectral flow between quantum superbands and Chern numbers c
2 computed by Avron et al.
Controllable fabrication of silver nanofilament for using as tip in tip-enhanced Raman spectroscopy
Authors: Phonrachom O , Pienpinijtham P , Sapcharoenkun C
Published: August 2022

Tip-enhanced Raman spectroscopy (TERS) is a technique offering chemical information at a single molecule level as well as chemical fingerprints with nanoscale spatial resolution. Currently, TERS tip fabrication in terms of size, shape, and stability has still been challenged due to its low reproducibility. In this work, electron beam irradiation and chemical bath deposition (CBD) were used to create a silver nanofilament (AgNF) on an atomic force microscope (AFM) tip, and it was further used as a TERS tip. Conditions, i.e., accelerated voltage and irradiation time, in the electron beam irradiation with different Ag thin film thicknesses in the production of the AgNF tip were investigated. The highest density of AgNF of the TERS probe was achieved with 52.5×109 NF/cm2 by using an accelerated voltage of 20 kV and an irradiation time of 20 minutes. This study will pave the way for the use of the AgNF tip as the TERS tip.
Maxwell’s equations for a mechano-driven, shape-deformable, charged-media system, slowly moving at an arbitrary velocity field v(
r
,t)
Authors: Wang Zhong Lin
Published: August 2022

The differential form of the Maxwell’s equations was first derived based on an assumption that the media are stationary, which is the foundation for describing the electro-magnetic coupling behavior of a system. For a general case in which the medium has a time-dependent volume, shape and boundary and may move at an arbitrary velocity field

v
(
r
,
t
)

and along a general trajectory, we derived the Maxwell’s equations for a mechano-driven slow-moving media system directly starting from the integral forms of four physics laws, which should be accurate enough for describing the coupling among mechano-electro-magnetic interactions of a general system in practice although it may not be Lorentz covarance. Our key point is directly from the four physics laws by describing all of the fields, the space and the time in the frame where the observation is done. The equations should be applicable to not only moving charged solid and soft media that has acceleration, but also charged fluid/liquid media, e.g., fluid electrodynamics. This is a step toward the electrodynamics in non-inertia frame of references. General strategies for solving the Maxwell’s equations for mechano-driven slowing moving medium are presented using the perturbation theory both in time and frequency spaces. Finally, approaches for the electrodynamics of moving media are compared, and related discussions are given about a few interesting questions.
Positivity of Riemann–Roch polynomials and Todd classes of hyperkähler manifolds
Authors: Jiang Chen
Published: August 2022

For a hyperkähler manifold

X
X

of dimension

2
n

2n

, Huybrechts showed that there are constants

a
0

a_0

,

a
2

a_2

, …,

a

2
n

a_{2n}

such that
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="chi left-parenthesis upper L right-parenthesis equals sigma-summation Underscript i equals 0 Overscript n Endscripts StartFraction a Subscript 2 i Baseline Over left-parenthesis 2 i right-parenthesis factorial EndFraction q Subscript upper X Baseline left-parenthesis c 1 left-parenthesis upper L right-parenthesis right-parenthesis Superscript i">

χ
(
L
)
=

∑

i
=
0

n

a

2
i

(
2
i
)
!

q
X

(

c
1

(
L
)

)

i

\begin{equation*} \chi (L) =\sum _{i=0}^n\frac {a_{2i}}{(2i)!}q_X(c_1(L))^{i} \end{equation*}

for any line bundle

L
L

on

X
X

, where

q
X

q_X

is the Beauville–Bogomolov–Fujiki quadratic form of

X
X

. Here the polynomial

∑

i
=
0

n

a

2
i

(
2
i
)
!

q

i

\sum _{i=0}^n\frac {a_{2i}}{(2i)!}q^{i}

is called the Riemann–Roch polynomial of

X
X

.

In this paper, we show that all coefficients of the Riemann–Roch polynomial of

X
X

are positive. This confirms a conjecture proposed by Cao and the author, which implies Kawamata’s effective non-vanishing conjecture for projective hyperkähler manifolds. It also confirms a question of Riess on strict monotonicity of Riemann–Roch polynomials.

In order to estimate the coefficients of the Riemann–Roch polynomial, we produce a Lefschetz-type decomposition of

t
d

1

/

2

(
X
)

\mathrm {td}^{1/2}(X)

, the root of the Todd genus of

X
X

, via the Rozansky–Witten theory following the ideas of Hitchin and Sawon, and of Nieper-Wißkirchen.
Mass spectrometry–guided discovery of new analogs of bicyclic phosphotriester salinipostin and evaluation of their monoacylglycerol lipase inhibitory activity
Authors: Kudo Yuta , Konoki Keiichi , Yotsu-Yamashita Mari
Published: August 2022

Natural products containing the highly unusual phosphotriester ring are known to be potent serine hydrolase inhibitors. The long-chain bicyclic enol-phosphotriester salinipostins (SPTs) from the marine actinomycete Salinispora have been identified as selective antimalarial agents. A potential regulatory function has been suggested for phosphotriesters based on their structural relationship with actinomycete signaling molecules and the prevalence of spt-like biosynthetic gene clusters across actinomycetes. In this study, we established a mass spectrometry–guided screening method for phosphotriesters focusing on their characteristic fragment ions. Applying this screening method to the SPT producer Salinispora tropica CNB-440, new SPT analogs (4-6) were discovered and their structures were elucidated by spectroscopic analyses. Previously known and herein-identified SPT analogs inhibited the activity of human monoacylglycerol lipase (MAGL), a key serine hydrolase in the endocannabinoid system, in the nanomolar range. Our method could be applied to the screening of phosphotriesters, potential serine hydrolase inhibitors and signaling molecules.
CPRiL: compound–protein relationships in literature
Authors: Qaseem Ammar , Günther Stefan
Published: August 2022

Newly discovered functional relationships of (bio-)molecules are a key component in molecular biology and life science research. Especially in the drug discovery field, knowledge of how small molecules associated with proteins plays a fundamental role in understanding how drugs or metabolites can affect cells, tissues and human metabolism. Finding relevant information about these relationships among the huge number of published articles is becoming increasingly challenging and time-consuming. On average, more than 25 000 new (bio-)medical articles are added to the literature database PubMed weekly. In this article, we present a new web server [compound–protein relationships in literature (CPRiL)] that provides information on functional relationships between small molecules and proteins in literature. Currently, CPRiL contains ∼465 000 unique names and synonyms of small molecules, ∼100 000 unique proteins and more than 9 million described functional relationships between these entities. The applied BioBERT machine learning model for the determination of functional relationships between small molecules and proteins in texts was extensively trained and tested. On a related benchmark, CPRiL yielded a high performance, with an F1 score of 84.3%, precision of 82.9% and recall of 85.7%.

Availability and implementation

CPRiL is freely available at https://www.pharmbioinf.uni-freiburg.de/cpril.

Supplementary information

Supplementary data are available at Bioinformatics online.
Structural cerebellar reserve positively influences outcome after severe stroke
Authors: Sadeghihassanabadi Fatemeh , Frey Benedikt M , Backhaus Winifried , Choe Chi-un , Zittel Simone , Schön Gerhard , Bönstrup Marlene , Cheng Bastian , Thomalla Götz , Gerloff Christian , Schulz Robert
Published: August 2022

The concept of brain reserve capacity positively influencing the process of recovery after stroke has been continuously developed in recent years. Global measures of brain health have been linked with a favourable outcome. Numerous studies have evidenced that the cerebellum is involved in recovery after stroke. However, it remains an open question whether characteristics of cerebellar anatomy, quantified directly after stroke, might have an impact on subsequent outcome after stroke. Thirty-nine first-ever ischaemic non-cerebellar stroke patients underwent MRI brain imaging early after stroke and longitudinal clinical follow-up. Structural images were used for volumetric analyses of distinct cerebellar regions. Ordinal logistic regression analyses were conducted to associate cerebellar volumes with functional outcome 3–6 months after stroke, operationalized by the modified Rankin Scale. Larger volumes of cerebellar lobules IV, VI, and VIIIB were positively correlated with favourable outcome, independent of the severity of initial impairment, age, and lesion volume (P < 0.01). The total cerebellar volume did not exhibit a significant structure-outcome association. The present study reveals that pre-stroke anatomy of distinct cerebellar lobules involved in motor and cognitive functioning might be linked to outcome after acute non-cerebellar stroke, thereby promoting the emerging concepts of structural brain reserve for recovery processes after stroke.
Chest pain workup in the presence of atrial fibrillation: impacts on troponin testing, myocardial infarction diagnoses, and long-term prognosis
Authors: Lancini Daniel , Greenslade Jaimi , Martin Paul , Prasad Sandhir , Atherton John , Parsonage William , Aldous Sally , Than Martin , Cullen Louise
Published: August 2022

Aims

Patients presenting to the emergency department (ED) with chest pain require evaluation for acute coronary syndrome (ACS). Atrial fibrillation (AF) can lead to troponin (cTn) elevation in the absence of ACS. There is limited evidence informing the impact of AF on the diagnostic performance of cTn testing for the diagnosis of Type 1 myocardial infarction (T1MI), or the association between AF and long-term outcomes in this context.

Methods and results

This study used the IMPACT and ADAPT study databases to compile a combined cohort of 3496 adults presenting to ED with chest pain between 2007 and 2014, with early cTn testing during ED workup. The mean age was 56.6 years, and 40.2% were female. Outcomes included adjudicated diagnoses for the index admission and mortality to 1-year after presentation. The specificity of initial cTn testing for T1MI diagnosis was lower for patients in AF compared with those not in AF (79.2% vs. 95.4%, P < 0.001), largely due to a relative increase in Type 2 myocardial infarction diagnoses. Sensitivity for T1MI did not differ between patients with or without AF (88.5% vs. 91.5%, P = 0.485). AF was associated with increased 1-year mortality (10.4% vs. 2.3%, P < 0.001), although this was not significant on multivariable analysis.

Conclusion

The specificity of serial cTn testing for the diagnosis of T1MI in patients presenting to ED with chest pain is reduced in the presence of AF. Further studies are needed to establish whether optimised cTn thresholds for patients with AF can improve workup and outcomes.
Haemolysis resolution after transcatheter valve in valve within a prior mitral annuloplasty ring: a case report
Authors: Bhardwaj Bhaskar , Golwala Harsh , Song Howard K , Lantz Gurion , Chadderdon Scott , Zahr Firas
Published: August 2022

Background

Transcatheter mitral valve in ring procedure has emerged as a minimally invasive alternative to re-do surgery among patients with failed mitral annuloplasty rings. Uncommonly, haemolysis presents as a complication after the percutaneous valvular procedures and often require aggressive measures to correct paravalvular leaks and mechanical collision.

Case summary

We report a case of an 82-year-old female who underwent a transcatheter valve in ring procedure (Edwards Sapien S3, Edwards Lifesciences) for symptomatic severe mitral regurgitation from a bioprosthetic annuloplasty ring failure complicated by acute haemolytic anaemia a week after the procedure manifesting as dark coloured urine, profound icterus, and acute renal injury. She was treated with a post-dilation balloon valvuloplasty leading to reduction in haemolysis, but the patient was readmitted with acute haemolysis episode again. At this time, a decision was made to perform a repeat valve in valve TMVR with a 29 mm S3 Edwards Sapien valve which led to a resolution of haemolysis.

Discussion

In this case, the leaflets of previously placed S3 valve sealed the blood flow through the valve frame thus diverting the blood flow away from the area of collision leading to resolution of haemolysis.
Temporal trends in atherosclerotic cardiovascular disease risk among U.S. adults. Analysis of the National Health and Nutrition Examination Survey, 1999–2018
Authors: Chobufo Muchi Ditah , Singla Atul , Rahman Ebad Ur , Michos Erin D , Whelton Paul K , Balla Sudarshan
Published: August 2022

Background

Atherosclerotic cardiovascular diseases are a significant cause of disability and mortality. Study of trends in cardiovascular risk at a population level helps understand the overall cardiovascular health and the impact of primary prevention efforts.

Aims

To assess trends in the estimated 10-year atherosclerotic cardiovascular disease (ASCVD) risk among U.S. adults from 1999–2000 to 2017–18 with no established cardiovascular disease (CVD).

Methods and results

Serial cross-sectional analysis of National Health and Nutrition Examination Survey (NHANES) data from 1999–2000 to 2017–18 (10 cycles), including 24 022 US adults aged 40–79 years with no reported ASCVD. ASCVD risk was assessed using the pooled cohort equations (PCEs). There was a significant temporal decline in the mean 10-year ASCVD risk from 13.5% (95% CI, 12.5–14.4) in 1999–2000 to 11.1% (10.5–11.7) in 2011–12 (Ptrend < 0.001) and to 12.0% (11.3–12.7) in 2017–2018 (overall Ptrend = 0.001), with the mean ASCVD risk score remaining stable from 2013–14 through 2017–2018 (Ptrend = 0.056). A declining trend in ASCVD risk was noted in females, non-Hispanic Blacks and those with income <3 times the poverty threshold with Ptrend of <0.001, 0.002, and 0.007, respectively. Mean total cholesterol and prevalence of smokers showed a downward trend (Ptrend <0.001 for both), whereas type 2 diabetes and mean BMI showed an upward trend (Ptrend < 0.001 for both).

Conclusions

The 20-year trend of ASCVD risk among NHANES participants 40–79 years, as assessed by the use of PCE, showed a non-linear downward trend from 1999–2000 to 2017–18. The initial and significant decline in estimated ASCVD risk from 1999–2000 to 2011–12 subsequently stabilized, with no significant change from 2013–14 to 2017–18. Mean BMI and prevalence of diabetes mellitus increased while mean serum cholesterol levels and prevalence of smoking declined during the study period. Our findings support invigoration of efforts aimed at prevention of CVD, including primordial prevention of CVD risk factors.
Rapid in vivo development of resistance to daptomycin in vancomycin-resistant Enterococcus faecium due to genomic alterations
Authors: Mollerup Sarah , Elmeskov Christine , Pinholt Mette , Sejersen Tobias S , Pedersen Martin S , Worning Peder , Frees Dorte , Westh Henrik
Published: August 2022

Daptomycin is a cyclic lipopeptide used in the treatment of vancomycin-resistant Enterococcus faecium (VREfm). However, the development of daptomycin-resistant VREfm challenges the treatment of nosocomial VREfm infections. Resistance mechanisms of daptomycin are not fully understood. Here, we analyzed the genomic changes leading to a daptomycin-susceptible VREfm isolate becoming resistant after 50 days of daptomycin and linezolid combination therapy. A total of seven isogenic VREfm isolates from the same patient (daptomycin-susceptible and daptomycin-resistant) were analyzed using Illumina whole genome sequencing, and two isolates were further characterized with Nanopore sequencing. One nonsynonymous SNP in the rpoC gene previously shown to harbor mutations in daptomycin-resistant VREfm was identified in the daptomycin-resistant isolates. Whole genome comparative analysis identified the loss of a 46.5 kb fragment, duplication of a 29.7 kb fragment, and integration of two plasmids upon acquisition of daptomycin resistance. Transmission electron microscopy showed similar alterations in cell morphology and cell wall structure as have previously been described in daptomycin-resistant E. faecalis.
Reversion is most likely under high mutation supply when compensatory mutations do not fully restore fitness costs
Authors: Pennings Pleuni S , Ogbunugafor C Brandon , Hershberg Ruth
Published: August 2022

The dynamics of adaptation, reversion, and compensation have been central topics in microbial evolution, and several studies have attempted to resolve the population genetics underlying how these dynamics occur. However, questions remain regarding how certain features—the evolution of mutators and whether compensatory mutations alleviate costs fully or partially—may influence the evolutionary dynamics of compensation and reversion. In this study, we attempt to explain findings from experimental evolution by utilizing computational and theoretical approaches toward a more refined understanding of how mutation rate and the fitness effects of compensatory mutations influence adaptive dynamics. We find that high mutation rates increase the probability of reversion toward the wild type when compensation is only partial. However, the existence of even a single fully compensatory mutation is associated with a dramatically decreased probability of reversion to the wild type. These findings help to explain specific results from experimental evolution, where compensation was observed in nonmutator strains, but reversion (sometimes with compensation) was observed in mutator strains, indicating that real-world compensatory mutations are often unable to fully alleviate the costs associated with adaptation. Our findings emphasize the potential role of the supply and quality of mutations in crafting the dynamics of adaptation and reversal, with implications for theoretical population genetics and for biomedical contexts like the evolution of antibiotic resistance.
Allele-specific alternative splicing of Drosophila Ribosomal protein S21 suppresses a lethal mutation in the Phosphorylated adaptor for RNA export (Phax) gene
Authors: Garcia Eric L
Published: August 2022

Genetic disruptions to the biogenesis of spliceosomal small-nuclear ribonucleoproteins in Drosophila cause wide-spread alternative splicing changes, including changes to the splicing of pre-mRNA for Ribosomal protein S21 (RpS21). Using a transposon mutant for the Phosphorylated adaptor for RNA export (Phax) gene, we demonstrate that changes in the splicing of RpS21 transcripts have a strong influence on the developmental progression of PhaxSH/SH mutants. Different alleles of the Drosophila RpS21 gene are circulating in common laboratory strains and cell lines. These alleles exhibit differences in RpS21 intron retention and splicing efficiency. Differences in the splicing of RpS21 transcripts account for prior conflicting observations of the phenotypic severity of PhaxSH/SH mutant stocks. The alleles uncover a strong splicing enhancer in RpS21 transcripts that can fully suppress the larval lethality and partially suppress the pupal lethality exhibited by PhaxSH/SH mutant lines. In the absence of the splicing enhancer, the splicing of RpS21 transcripts can be modulated in trans by the SR-rich B52 splicing factor. As PhaxSH/SH mutants exhibit wide-spread splicing changes in transcripts for other genes, findings here establish the importance of a single alternative splicing event, RpS21 splicing or intron retention, to the developmental progression of Drosophila.