bluuebunny/crossref_metadata_2025 huggingface dataset:
Knowledge Representation and Management: Interest in New Solutions for Ontology Curation
Authors: Dhombres Ferdinand , Charlet Jean ,   Section Editors for the IMIA Yearbook Section on Knowledge Representation and Management
Published: September 2021

Objective: To select, present and summarize some of the best papers in the field of Knowledge Representation and Management (KRM) published in 2020.

Methods: A comprehensive and standardized review of the medical informatics literature was performed to select the most interesting papers of KRM published in 2020, based on PubMed queries. This review was conducted according to the IMIA Yearbook guidelines.

Results: Four best papers were selected among 1,175 publications. In contrast with the papers selected last year, the four best papers of 2020 demonstrated a significant focus on methods and tools for ontology curation and design. The usual KRM application domains (bioinformatics, machine learning, and electronic health records) were also represented.

Conclusion: In 2020, ontology curation emerges as a significant topic of research interest. Bioinformatics, machine learning, and electronics health records remain significant research areas in the KRM community with various applications. Knowledge representations are key to advance machine learning by providing context and to develop novel bioinformatics metrics. As in 2019, representations serve a great variety of applications across many medical domains, with actionable results and now with growing adhesion to the open science initiative.
The Clinical Information Systems Response to the COVID-19 Pandemic
Authors: Reeves J. Jeffery , Pageler Natalie M. , Wick Elizabeth C. , Melton Genevieve B. , Tan Yu-Heng Gamaliel , Clay Brian J. , Longhurst Christopher A.
Published: September 2021

Objective: The year 2020 was predominated by the coronavirus disease 2019 (COVID-19) pandemic. The objective of this article is to review the areas in which clinical information systems (CIS) can be and have been utilized to support and enhance the response of healthcare systems to pandemics, focusing on COVID-19.

Methods: PubMed/MEDLINE, Google Scholar, the tables of contents of major informatics journals, and the bibliographies of articles were searched for studies pertaining to CIS, pandemics, and COVID-19 through October 2020. The most informative and detailed studies were highlighted, while many others were referenced.

Results: CIS were heavily relied upon by health systems and governmental agencies worldwide in response to COVID-19. Technology-based screening tools were developed to assist rapid case identification and appropriate triaging. Clinical care was supported by utilizing the electronic health record (EHR) to onboard frontline providers to new protocols, offer clinical decision support, and improve systems for diagnostic testing. Telehealth became the most rapidly adopted medical trend in recent history and an essential strategy for allowing safe and effective access to medical care. Artificial intelligence and machine learning algorithms were developed to enhance screening, diagnostic imaging, and predictive analytics - though evidence of improved outcomes remains limited. Geographic information systems and big data enabled real-time dashboards vital for epidemic monitoring, hospital preparedness strategies, and health policy decision making. Digital contact tracing systems were implemented to assist a labor-intensive task with the aim of curbing transmission. Large scale data sharing, effective health information exchange, and interoperability of EHRs remain challenges for the informatics community with immense clinical and academic potential. CIS must be used in combination with engaged stakeholders and operational change management in order to meaningfully improve patient outcomes.

Conclusion: Managing a pandemic requires widespread, timely, and effective distribution of reliable information. In the past year, CIS and informaticists made prominent and influential contributions in the global response to the COVID-19 pandemic.
Fermi level modulation of boron nitride nanosheets by vacancy driven compressive strain
Authors: Mahanta Tanmay , Mohanty Tanuja
Published: September 2021

In this Letter, the compressive strain-assisted reduction of work function (WF) of boron nitride nanosheets (BNNSs) has been presented. For this purpose, a 30 keV Au−1 ion beam was irradiated on a high-quality BNNS deposited on a Si substrate. Before ion irradiation, the pristine BNNSs were characterized by Raman spectroscopy and UV-Vis absorption spectroscopy for the estimation of its number of layers and bandgap. The scanning electron microscopic images confirm a layer-like structure in a pristine BNNS. An x-ray diffraction (XRD) peak corresponding to the (002) plane of BNNSs appears at an angle of 26°. Shifting of the XRD peak toward higher angle with increasing fluence indicates the presence of a compressive strain in BNNSs. Scanning kelvin probe microscopy was used to map the work function of the surface of BNNSs, and it turned out that the WF decreases with increasing the dose of ions. The possible explanation of compressive strain generation by Au−1 irradiation on BNNSs is discussed using the SRIM-2013 Monte Carlo simulation. The value of strain, calculated from the work function values, qualitatively agrees with the XRD result.
2D MHD simulation of spontaneous magnetic fields generated during interaction of 1315.2-nm laser radiation with copper slabs at 1016 W/cm2
Authors: Jach K. , Pisarczyk T. , Stępniewski W. , Świerczyński R. , Krasa J. , Chodukowski T. , Rusiniak Z. , Zaraś-Szydłowska A. , Dostal J. , Dudzak R. , Juha L. , Kochetkov Iu. , Krupka M. , Borodziuk S.
Published: September 2021

Multidimensional modeling of phenomena and processes occurring during the expansion of the laser-produced plasma for different irradiation conditions related to both the laser beam parameters and the target constructions is a very complex issue, especially when modeling requires consideration of kinetic processes associated with the development of various types of microscopic instability. Multidimensional PIC codes create such a possibility, but their use is limited to modeling phenomena even in a very narrow timescale due to the limited computational capabilities of current supercomputers. For this reason, the paper attempts to interpret the results of the spontaneous magnetic field (SMF) measurements obtained during the PALS (Prague Asterix Laser System) experiment [Pisarczyk et al., AIP Adv. 10, 115201 (2020); Pisarczyk et al., Phys. Plasmas 22, 102706 (2015)] based on the 2D magneto-hydrodynamic (MHD) model [Jach et al., Computer Modeling of Dynamic Interaction of Bodies by Free Point Method (PWN, Warsaw, 2011)]. The MHD equations were used with included arbitrary (i) current of hot electrons treating it as an additional external current and (ii) ion-sound instability responsible for the increase in anomalous resistance in areas with high temperature and low-density plasma. The spatial distribution of magnetic fields and current density obtained from 2D modeling are in acceptable agreement with the experimental results [Pisarczyk et al., Plasma Phys. Controlled Fusion 62, 115020 (2020); Zaraś-Szydłowska et al., AIP Adv. 10, 115201 (2020); Pisarczyk et al., Phys. Plasmas 22, 102706 (2015)]. The inclusion of temporal changes in anomalous resistance in modeling allowed us to explain the persistence of high SMF amplitude at the level of several megagauss after the laser pulse ended due to the effect of magnetic field freezing.
Design and expected performance of a variable-radii sinusoidal spiral x-ray spectrometer for the National Ignition Facility
Authors: Pablant N. A. , Bitter M. , Efthimion P. C. , Gao L. , Hill K. W. , Kraus B. F. , Kring J. , MacDonald M. J. , Ose N. , Ping Y. , Schneider M. B. , Stoupin S. , Yakusevitch Y.
Published: September 2021

A novel high-resolution x-ray spectrometer for point-like emission sources has been developed using a crystal shape having both a variable major and a variable minor radius of curvature. This variable-radii sinusoidal spiral spectrometer (VR-Spiral) allows three common spectrometer design goals to be achieved simultaneously: 1. reduction of aberrations and improved spectral (energy) resolution, 2. reduction of source size broadening, and 3. use of large crystals to improve total throughput. The VR-Spiral concept and its application to practical spectrometer design are described in detail. This concept is then used to design a spectrometer for an extreme extended x-ray absorption fine structure experiment at the National Ignition Facility looking at the Pb L3 absorption edge at 13.0352 keV. The expected performance of this VR-Spiral spectrometer, both in terms of energy resolution and spatial resolution, is evaluated through the use of a newly developed raytracing tool, xicsrt. Finally, the expected performance of the VR-Spiral concept is compared to that of spectrometers based on conventional toroidal and variable-radii toroidal crystal geometries showing a greatly improved energy resolution.
A single nucleobase tunes nonradiative decay in a DNA-bound silver cluster
Authors: Zhang Yuyuan , He Chen , de La Harpe Kimberly , Goodwin Peter M. , Petty Jeffrey T. , Kohler Bern
Published: September 2021

DNA strands are polymeric ligands that both protect and tune molecular-sized silver cluster chromophores. We studied single-stranded DNA C4AC4TC3XT4 with X = guanosine and inosine that form a green fluorescent Ag106+ cluster, but these two hosts are distinguished by their binding sites and the brightness of their Ag106+ adducts. The nucleobase subunits in these oligomers collectively coordinate this cluster, and fs time-resolved infrared spectra previously identified one point of contact between the C2–NH2 of the X = guanosine, an interaction that is precluded for inosine. Furthermore, this single nucleobase controls the cluster fluorescence as the X = guanosine complex is ∼2.5× dimmer. We discuss the electronic relaxation in these two complexes using transient absorption spectroscopy in the time window 200 fs–400 µs. Three prominent features emerged: a ground state bleach, an excited state absorption, and a stimulated emission. Stimulated emission at the earliest delay time (200 fs) suggests that the emissive state is populated promptly following photoexcitation. Concurrently, the excited state decays and the ground state recovers, and these changes are ∼2× faster for the X = guanosine compared to the X = inosine cluster, paralleling their brightness difference. In contrast to similar radiative decay rates, the nonradiative decay rate is 7× higher with the X = guanosine vs inosine strand. A minor decay channel via a dark state is discussed. The possible correlation between the nonradiative decay and selective coordination with the X = guanosine/inosine suggests that specific nucleobase subunits within a DNA strand can modulate cluster–ligand interactions and, in turn, cluster brightness.
Versatile semi-batch apparatus for manometric measurement of gas–solid reaction rates
Authors: Heidlage Michael G. , Aloi M. J. , Safarik D. J.
Published: September 2021

We describe the design, construction, operation, and performance of a simple and versatile semi-batch reactor that is especially useful for measurement of gas/solid reaction rates at pressures in the range of 1 mTorr to 1500 Torr. The reactor operates by repeatedly imposing small AC modulations of reactant gas pressure on top of a much larger DC pressure background. Based on the rate of pressure relaxation following each AC pulse, the reaction rate is determined. Our design is characterized by modular construction from off-the-shelf, ultra-high-vacuum-compatible components, which facilitate easy retrofitting and adaptation to a range of experimental conditions. Automated experiment control and data acquisition is accomplished via a custom National Instruments© LabView virtual instrument. Data analysis is automated using a custom series of Mathworks© Matlab scripts. We demonstrate reactor performance through measurements of hydrogenation kinetics for a composite H2 getter material consisting of 1,4-bis(phenylethynyl)benzene mixed with a palladium/carbon catalyst.
Guide field effects on the distribution of plasmoids in multiple scale reconnection
Authors: Majeski Stephen , Ji Hantao , Jara-Almonte Jonathan , Yoo Jongsoo
Published: September 2021

The effects of a finite guide field on the distribution of plasmoids in high-Lundquist-number current sheets undergoing magnetic reconnection in large plasmas are investigated with statistical models. Merging of plasmoids is taken into account either assuming that guide field flux is conserved resulting in nonforce-free profiles in general, or that magnetic helicity is conserved and Taylor relaxation occurs to convert part of the summed guide field flux into reconnecting field flux toward minimum energy states resulting in force-free profiles. It is found that the plasmoid distribution in terms of reconnecting field flux follows a power law with index 7/4 or 1 depending on whether merger frequencies are independent of or dependent on their relative velocity to the outflow speed, respectively. This result is approximately the same for the force-free and nonforce-free models, with nonforce-free models exhibiting indices of 2 and 1 for the same velocity dependencies. Distributions in terms of guide field flux yield indices of 3/2 for the nonforce-free model regardless of velocity dependence. This is notably distinct from the indices of 11/8 and 1 for the force-free models independent of and dependent on velocity, respectively. At low guide field fluxes, the force-free models exhibit a second power law index of 1/2 due to nonconstant flux growth rates. The velocity-dependent force-free model predicts the production of slightly more rapidly moving large guide field flux plasmoids which are supported by observational evidence of flux ropes with strong core fields. Implications are discussed on particle acceleration via Fermi processes.
Equation of motion coupled-cluster study of core excitation spectra II: Beyond the dipole approximation
Authors: Park Young Choon , Perera Ajith , Bartlett Rodney J.
Published: September 2021

We present the time-independent (TI) and time-dependent (TD) equation of motion coupled-cluster (EOM-CC) oscillator strengths not limited to those obtained by the dipole approximation. For the conventional TI-EOM-CC, we implement all the terms in the multipole expansion through second order that contributes to the oscillator strength. These include contributions such as magnetic dipole, electric quadrupole, electric octupole, and magnetic quadrupole. In TD-EOM-CC, we only include the quadrupole moment contributions. This augments our previous work [Y. C. Park, A. Perera, and R. J. Bartlett, J. Chem. Phys. 151, 164117 (2019)]. The inclusion of the quadrupole contributions (and all the other contributions through second order in the case of TI-EOM-CCSD) enables us to obtain the intensities for the pre-edge transitions in the metal K-edge spectra, which are dipole inactive. The TI-EOM-CCSD and TD-EOM-CCSD spectra of Ti4+ atoms are used to showcase the implementation of the second-order oscillator strengths. The origin of 1s → e and 1s → t2 in core spectra from iron tetrachloride and titanium tetrachloride is discussed and compared with the experiment.
Flux-driven algebraic damping of m = 2 diocotron mode
Authors: Chim Chi Yung , O'Neil Thomas M.
Published: September 2021

Experiments with pure electron plasmas in a Malmberg–Penning trap have observed linear in time, algebraic damping of m = 2 diocotron modes. Transport due to small field asymmetries produces a low-density halo of electrons moving radially outward from the plasma core, and the mode damping begins when the halo reaches the resonant radius of the mode. The damping rate is proportional to the flux of halo particles through the resonant layer. The damping is related to, but distinct from spatial Landau damping in which a linear wave–particle resonance produces exponential damping. This paper reports an analytic theory that captures the main signatures reported for this novel damping, namely, that the damping begins when the halo particles reach the resonant radius and that the damping is algebraic in time with nearly constant damping rate. The model also predicts a nonlinear frequency shift. The model provides two ways to think about the damping. It results from a transfer of canonical angular momentum from the mode to halo particles being swept by the mode field through the nonlinear cat's eye orbits of the resonant region. More mechanistically, the electric field produced by the perturbed charge density of the resonant particles acts back on the plasma core causing E×B drift that gives rise to the damping and nonlinear frequency shift.
Antimony segregation in an InAs/InAs1−xSbx superlattice grown by metalorganic chemical vapor deposition
Authors: Yang Qun , Yuan Renliang , Wang Lingling , Shi Ruikai , Zuo Jian-Min
Published: September 2021

Metal organic chemical vapor deposition (MOCVD) and molecular beam epitaxy (MBE) are two versatile growth techniques that can readily produce multilayer structures with atomic-level precision control, which have found broad applications in technology. However, compared to MBE, MOCVD growth involves the surface reaction of metal-organic precursor compounds, which changes during film deposition. Consequently, a thorough investigation on the chemical profile layer-by-layer is critical for optimizing MOCVD film performance. Here, we examine Sb segregation in an MOCVD-grown InAs/InAs1−xSbx superlattice by analyzing composition and lattice strain at atomic resolution using scanning transmission electron microscopy and compare with the previously reported MBE growth results. Our findings show a different Sb profile along the growth direction in MOCVD, with the segregation coefficient being higher at the InAsSb-on-InAs interface (0.807 ± 0.021) than at the InAs-on-InAsSb interface (0.695 ± 0.009), giving rise to asymmetric composition and lattice strain profiles unlike those obtained with MBE. Furthermore, we obtain direct evidence of Sb clusters with size of ∼1–3 nm and Sb ordering within the InAs1−xSbx layer, which is largely absent in the reported MBE growth. These findings demonstrate the concurrent interplay between surface segregation, surface reconstruction, and surface reaction that is unique to MOCVD growth with broad implications on preparing Sb-containing quantum materials.
Realization of electrically driven AlGaN micropillar array deep-ultraviolet light emitting diodes at 286 nm
Authors: Melanson Bryan , Hartensveld Matthew , Liu Cheng , Zhang Jing
Published: September 2021

We report on the realization of top-down fabricated, electrically driven, deep-ultraviolet (DUV) AlGaN micropillar array light emitting diodes (LEDs) with high output power density. Ordered arrays of micropillars with the inverse-taper profile were formed from an AlGaN epitaxial stack (epistack) using a Ni-masked Cl2 plasma dry etch and KOH-based wet etching. Following deposition of the n-contact, polydimethylsiloxane was spin-coated and etched-back to reveal the tips of the pillars to allow for formation of the p-contact. The DUV LEDs were tested at the wafer-level using a manual probe station to characterize their electrical and optical properties, revealing stable electroluminescence at 286 nm with a narrow 9-nm linewidth. Optical output power was found to be linearly related to current density, with output power densities up to 35 mW/cm2, comparable to the results reported for epitaxially grown DUV nanowire LEDs. Simulations revealed that the inverse-taper profile of the micropillars could lead to large enhancements in light extraction efficiency (ηEXT) of up to 250% when compared to micropillars with vertical sidewalls. The realization of ordered, electrically driven, top-down fabricated micropillar DUV LEDs with competitive output power represents an important step forward in the development of high-efficiency, scalable DUV emitters for a wide range of applications.
A direct numerical simulation study of flow modulation and turbulent sedimentation in particle-laden downward channel flows
Authors: Yang Bo , Peng Cheng , Wang Guichao , Wang Lian-Ping
Published: September 2021

Fully resolved direct numerical simulations of turbulent downward channel flow laden with finite-size spherical particles are performed using the lattice Boltzmann method. Unlike upward particle-laden channel flows, the potential energy of settling particles serves as the driving force in the downward channel flows. Furthermore, the particles have an overall positive slip velocity at the center which causes the lateral hydrodynamic force to drive particles away from the center region. Both changes in the flow driving mechanism and the particle distribution affect the details of turbulence modulation in the downward channel, when compared to the upward channel flow. In this study, we focus on the effect of different particle terminal velocities, i.e., different particle settling Reynolds numbers, on the turbulent modulation of particle-laden downward channel flows. Indeed, the simulation results for downward channel flow show larger local particle concentration in the near-wall region, relative to the upward channel. It is also found that the level of particle near-wall accumulation increases with the particle terminal velocity. Opposite to the upward channel flows, the fluid-phase mean velocity in the downward channel flows is increased by heavy particles in the channel center, but reduced in the buffer layer. The reduction of mean velocity in the buffer layer is caused by the particle accumulation in low-speed streak regions. For the largest particle settling Reynolds number case (ReT = 30) investigated, strong accumulation of particles in the buffer layer interrupts the near-wall turbulence structures and thus leads to the reductions of fluid turbulence intensity and Reynolds stress.
Simplification of plasma chemistry by means of vital nodes identification
Authors: Sun Bowen , Liu Dingxin , Liu Yifan , Luo Santu , Zhang Mingyan , Zhang Jishen , Yang Aijun , Wang Xiaohua , Rong Mingzhe
Published: September 2021

Cold atmospheric plasmas have great application potential due to their production of diverse types of reactive species, so understanding the production mechanism and then improving the production efficiency of the key reactive species are very important. However, plasma chemistry typically comprises a complex network of chemical species and reactions, which greatly hinders identification of the main production/reduction reactions of the reactive species. Previous studies have identified the main reactions of some plasmas via human experience, but since plasma chemistry is sensitive to discharge conditions, which are much different for different plasmas, widespread application of the experience-dependent method is difficult. In this paper, a method based on graph theory, namely, vital nodes identification, is used for the simplification of plasma chemistry in two ways: (1) holistically identifying the main reactions for all the key reactive species and (2) extracting the main reactions relevant to one key reactive species of interest. This simplification is applied to He + air plasma as a representative, chemically complex plasma, which contains 59 species and 866 chemical reactions, as reported previously. Simplified global models are then developed with the key reactive species and main reactions, and the simulation results are compared with those of the full global model, in which all species and reactions are incorporated. It was found that this simplification reduces the number of reactions by a factor of 8–20 while providing simulation results of the simplified global models, i.e., densities of the key reactive species, which are within a factor of two of the full global model. This finding suggests that the vital nodes identification method can capture the main chemical profile from a chemically complex plasma while greatly reducing the computational load for simulation.
Accurate prediction and measurement of vibronic branching ratios for laser cooling linear polyatomic molecules
Authors: Zhang Chaoqun , Augenbraun Benjamin L. , Lasner Zack D. , Vilas Nathaniel B. , Doyle John M. , Cheng Lan
Published: September 2021

We report a generally applicable computational and experimental approach to determine vibronic branching ratios in linear polyatomic molecules to the 10−5 level, including for nominally symmetry-forbidden transitions. These methods are demonstrated in CaOH and YbOH, showing approximately two orders of magnitude improved sensitivity compared with the previous state of the art. Knowledge of branching ratios at this level is needed for the successful deep laser cooling of a broad range of molecular species.
Athletes with unilateral patellar tendinopathy have increased subsequent lower extremity musculoskeletal injury risk
Authors: Fendri Thouraya , Rebai Haithem , Harrabi Mohammed Achraf , Chaari Fatma , Boyas Sébastien , Beaune Bruno , Sahli Sonia
Published: September 2021

This study aimed to investigate static and dynamic postural balance inter‐limb asymmetries in athletes with unilateral patellar tendinopathy (UPT) and estimate subsequent lower extremity musculoskeletal injury risk compared to controls. Twenty‐eight athletes with UPT were recruited. Twenty‐eight healthy athletes served as controls. Static postural balance inter‐limb asymmetry (symmetry index: SI) was assessed based on differences in the mean centre of pressure (CoP) velocity (CoPv) values between the affected leg (AL) and non‐affected leg (NAL) for the UPT group, and the dominant leg (DL) and non‐dominant leg (NDL) for controls. Outcome variables were dynamic postural balance, assessed with inter‐limb asymmetry using the Y Balance Test (YBT), and injury risk. In static balance, SI values were significantly (P<0.001) higher in the UPT group compared to controls. In dynamic balance, normalized inter‐limb asymmetry values were also significantly higher in athletes with UPT compared to controls in anterior (P<0.001), posteromedial (P<0.001) and posterolateral (P<0.01) directions, and in the composite score (P<0.001). Furthermore, the incidence of sustaining a non‐contact lower extremity injury during the follow‐up period (10 months) was significantly higher (P<0.05) in the UPT group compared to controls. Athletes with UPT had postural balance inter‐limb asymmetries. Moreover, they had increased subsequent lower extremity musculoskeletal injury risk compared to controls. Since most athletes with UPT continue to train and compete, adequate training and rehabilitation programmes should be implemented to prevent potential subsequent injury occurrence.
Past, present and future—sample environments for materials research studies in scattering and spectroscopy; a UK perspective
Authors: Terrill Nicholas J , Dent Andrew J , Dobson Barry , Beale Andrew M , Allen Lisa , Bras Wim
Published: September 2021

Small angle x-ray scattering and x-ray absorption fine structure are two techniques that have been employed at synchrotron sources ever since their inception. Over the course of the development of the techniques, the introduction of sample environments for added value experiments has grown dramatically. This article reviews past successes, current developments and an exploration of future possibilities for these two x-ray techniques with an emphasis on the developments in the United Kingdom between 1980–2020.
Coupling-inspired metasurfaces for polarization-correlation customizable absorption
Authors: Li Yongfeng , Pang Yongqiang , Zheng Lin , Chen Hongya , Feng Mingde , Wang Jiafu , Zhang Jieqiu , Qu Shaobo
Published: September 2021

Polarization-correlation customizable metasurface absorbers based on circular dichroism (CD) meta-atoms were proposed in this paper, of which the polarization-correlation can be altered by controlling the coupling effect between the CD meta-atoms with the same chirality. CD meta-atoms implemented via introducing resistance film into chiral resonators were firstly proposed. Wideband, high-efficiency left-handed/right-handed CD meta-atoms were demonstrated, respectively, for which the left-handed/right-handed circularly polarized (LCP/RCP) incident wave was strongly absorbed but the RCP/LCP incident wave was reflected into LCP/RCP wave with high efficiency. The metasurface absorber consisting of CD-meta-atom pairs were put forward for polarization-correlation customizable absorption. The coupling between two CD meta-atoms was investigated by theoretical and simulation analysis, which can be manipulated by controlling the orientation angles of the CD meta-atoms. As a proof-of-concept, a polarization-insensitive absorber utilizing a C4 2 × 2 CD-meta-atom pair was designed, simulated and measured. Attributed to the strong coupling between the four CD meta-atoms, both LCP and RCP wave were strongly absorbed in a wide frequency range from 8 GHz to 20 GHz. This paves a new way for designing wideband metasurfaces with polarization-correlation customizable performance.
A probabilistic transcranial magnetic stimulation localization method
Authors: Kataja Juhani , Soldati Marco , Matilainen Noora , Laakso Ilkka
Published: September 2021

Objective. Transcranial magnetic stimulation (TMS) can be used to safely and noninvasively activate brain tissue. However, the characteristic parameters of the neuronal activation have been largely unclear. In this work, we propose a novel neuronal activation model and develop a method to infer its parameters from measured motor evoked potential signals. Approach. The connection between neuronal activation due to an induced electric field and a measured motor threshold is modeled. The posterior distribution of the model parameters are inferred from measurement data using Bayes’ formula. The measurements are the active motor thresholds obtained with multiple stimulating coil locations, and the parameters of the model are the location, preferred direction of activation, and threshold electric field value of the activation site. The posterior distribution is sampled using a Markov chain Monte Carlo method. We quantify the plausibility of the model by calculating the marginal likelihood of the measured thresholds. The method is validated with synthetic data and applied to motor threshold measurements from the first dorsal interosseus muscle in five healthy participants. Main results. The method produces a probability distribution for the activation location, from which a minimal volume where the activation occurs with 95% probability can be derived. For eight or nine stimulating coil locations, the smallest such a volume obtained was approximately 100 mm3. The 95% probability volume intersected the pre-central gyral crown and the anterior wall of the central sulcus, and the preferred direction was perpendicular to the central sulcus, both findings being consistent with the literature. Furthermore, it was not possible to rule out if the activation occurred either in the white or grey matter. In one participant, two distinct activations sites were found while others exhibited a unique site. Significance. The method is both generic and robust, and it lays a foundation for a framework that enables accurate analysis and characterization of TMS activation mechanisms.
Designing and pilot testing a novel high-definition transcranial burst electrostimulation device for neurorehabilitation
Authors: Wang Shun-Min Samuel , Huang Yi-Jing , Chen Jia-Jin Jason , Wu Chun-Wei , Chen Chien-An , Lin Che-Wei , Nguyen Van-Truong , Peng Chih-Wei
Published: September 2021

Objective.Non-invasive brain stimulation has been promoted to facilitate neuromodulation in treating neurological diseases. Recently, high-definition (HD) transcranial electrical stimulation and a novel electrical waveform combining a direct current (DC) and theta burst stimulation (TBS)-like protocol were proposed and demonstrated high potential to enhance neuroplastic effects in a more-efficient manner. In this study, we designed a novel HD transcranial burst electrostimulation device and to preliminarily examined its therapeutic potential in neurorehabilitation.Approach.A prototype of the transcranial burst electrostimulation device was developed, which can flexibly output a waveform that combined a DC and TBS-like protocol and can equally distribute the current into 4 × 1 HD electrical stimulation by automatic impedance adjustments. The safety and accuracy of the device were then validated in a series ofin vitroexperiments. Finally, a pilot clinical trial was conducted to assess its clinical safety and therapeutic potential on upper-extremity rehabilitation in six patients with chronic stroke, where patients received either active or sham HD transcranial burst electrostimulation combined with occupational therapy three times per week for four weeks.Main results.The prototype was tested, and it was found to comply with all safety requirements. The output parameters were accurate and met the clinical study needs. The pilot clinical study demonstrated that the active HD transcranial burst electrostimulation group had greater improvement in voluntary motor function and coordination of the upper extremity than the sham control group. Additionally, no severe adverse events were noted, but slight skin redness under the stimulus electrode immediately after stimulation was seen.Conclusions.The results demonstrated the feasibility of incorporating the HD electrical DC and TBS-like protocol in our device; and the novel neuromodulatory device produced positive neurorehabilitation outcomes in a safe fashion, which could be the basis for the future clinical implementation for treating neurological diseases.

Trial registration:ClinicalTrials.gov Identifier: NCT04278105. Registered on 20 February 2020.
Spatial distribution of bottom sediments of the near-dam ples of Kuibyshev Reservoir
Authors: Turutina T V , Rakhuba A V , Shmakova M V
Published: September 2021

The composition of bottom sediments and the patterns of their spatial distribution are determined by external (type of underlying surface of the catchment area, anthropogenic development, intensity of soil erosion) and internal (water regime, intensity of water exchange, morphometry of the basin) factors. The analysis of the granulometric composition of the bottom sediments of the near-dam ples of the Kuibyshev Reservoir showed the relative uniformity of the ples soil in terms of size. At the same time, depending on the location of the sampling points, certain patterns of distribution of the size of bottom sediments in space are traced.
Kuibyshev reservoir shore transformation as a factor of archaeological heritage objects destruction
Authors: Gainullin I I , Usmanov B M , Sharipova D R , Bagautdinova L N
Published: September 2021

The article presents the results of long-term research carried out in the shoreline zone of the Kuibyshev reservoir, at the location of the Izmer’s complex of multitemporal archeological sites, territory the Republic of Tatarstan. “Beganchik” Paleolithic site and fortified settlement of Bolgar period “Devichiy Gorodok” were selected for detailed study. The assessment of the shoreline transformation has been carried out with the use of remote sensing data, advanced methods of field survey and geoinformation analysis. As a result the most dynamic areas have been identified. In the work, were used archival aerial images, high-resolution satellite images and results of field surveys.
The structure of currents and water exchange in the overgrowing shallows
Authors: Poddubnyi S A , Kutuzov A V , Tsvetkov A I
Published: September 2021

The morphometric characteristics and bottom topography of typical shallows behind the island are characterized. The long – term and seasonal dynamics of the water level in the Rybinsk reservoir during the period from 1947 to 2020 is considered. The periods of fluctuations of the main hydrometeorological parameters in relation to the investigated section of the reservoir are shown. Based on archival and modern observation data on the structure of currents, the patterns of water transport and water exchange in the shallows are investigated, taking its seasonal overgrowth with macrophytes into account.
Influence of post-pyrogenic successions of the forests of the Urals on the formation of maximum rainfall flood discharges
Authors: Ye Klimenko D , Cherepanova E S , Khomyleva A A
Published: September 2021

The issues of losses on the crowns of forest stands in the conditions of forest successions after fires and associated changes in the maximum discharge of rainfall floods are considered. The results of complex field, experimental work, deterministic modelling are presented. It has been established that with the complete burnout of forests in the catchment, the maximum flow rates can increase by 40% compared to the initial state of the forests, and with the restoration of forests, the maximum flow rates of floods again decrease by 15-20% over a 20-year period.
Assessment of the Kuybyshev Reservoir bed state: a case study
Authors: Khomyakov P V , Usmanov B M
Published: September 2021

The generalized results of the Kuybyshev Reservoir bed relief survey using modern methods are presented on the example of two sites. Sakony site area is located on the low left bank of the Kuybyshev Reservoir in the place of sand and gravel mix extraction, Sviyazhsk site – around the cultural heritage object Sviyazhsk island-town. The change in the bottom topography was monitored using the Interferometric Side-Scan Sonar and the HyScan software. Bathymetric maps and transverse profiles for study sites were built. A description of the bottom relief in the studied areas is given. As a result, reservoir bottom survey technique was developed to update its morphometry, possibility of obtained data application is discussed.
Flow rate regime of the Western Urals’s rivers
Authors: Mikova K D , Managadze A K
Published: September 2021

The flow rate is one of the most important elements of the river’s water regime. Establishing patterns in river flow rates’ changes within a year and by season is of great importance for the hydrological forecasts for spring floods, rain floods and hydrological calculations. By now, there are few publications on this area, both in Russia and abroad. The initial data were divided into 5 hydrological seasons – winter and summer low water, rise and fall of spring floods and autumn rain floods. For each season, an analysis of river flow rate over a period (1936-2013) was done. The average flow rate in rivers varied greatly depending on the water regime’ phase and the type of terrain in which the river flows. For all seasons, the amplitude of fluctuations in the flow rate on the plain rivers is less than on the mountain ones. So, in mountain rivers, flow rates vary from 0.04 to 2.42 m/s, and on flat rivers from 0.02 to 1.43 m/s. As well the pairwise and multiple correlation coefficients of flow rates for each morphometric and catchment characteristics were calculated. The highest correlation coefficients were obtained for the dependency between the average flow rate and the watershed elevation (0.30-0.75) and the watershed slope (0.42-0.76). The multiple correlation coefficients between the average flow rate and all catchment’s morphometric characteristics varied from 0.97 to 0.99. Results verification on an independent data demonstrated that the relative error was on average 2%.
Assessment of the landslide process intensity on the bank of the Kuybyshev Reservoir using instrumental methods
Authors: Gafurov A M , Usmanov B M , Yermolayev O P
Published: September 2021

The aim of the work was to survey and monitor dangerous exogeodynamic processes on the shoreline of the Kuibyshev reservoir. Field instrumental studies were used as the main method, including topo-geodetic survey of key morphological elements of the slope with ground control points, video and photo recording of the processes. Since 2019, unmanned aerial vehicle surveys have been chosen as the main method of research. The paper presents the results of long-term studies of the local landslide near Tetyushi, Republic of Tatarstan. As a result of 2003-2006 situational plans processing and results of UAV survey in 2019 quantitative data on the intensity of slope processes in the mass landslide were obtained.
Urban impact on water quality in the rivers of Central Russia
Authors: Georgiadi A G , Sharapova E O , Danilenko A O
Published: September 2021

Comparative analysis of the urban impact on water quality in the main rivers of Central Russia has been performed based on hydrochemical observations dataset for the period 2005-2019. It was obtained from monitoring results at the gauging stations located upstream and downstream of 11 cities in the studied region. The pollution level was estimated by comparison of the annually-averaged concentration values for 43 water quality indicators with their defined maximum permissible concentrations. The most substantial growth in concentrations downstream of the cities compared to their upstream values was revealed for heavy metals, nitrogen compounds, phosphates and oil products. A much less significant negative impact was imposed by cities on transparency, oxygen and major ions content. The cities were ranked by the total number of hydrochemical indicators which concentrations 1) increase downstream of cities, 2) exceed the maximum permissible concentrations before and after entering cities, 3) exceed the maximum permissible concentration before and after entering cities while sufficiently increasing (> 10%) at the downstream station. Additionally, the indicators were identified that experienced the most considerable impact from the urban areas. Among the studied cities, three groups were identified differing from each other in the degree of impact on the river water quality.
Mathematical modelling of spatial-temporal variability of phosphorus content and phytoplankton development in the Kuibyshev reservoir
Authors: Rakhuba A V
Published: September 2021

The article is dedicated to simulation of phytoplankton biomass growth dynamics amidst flow control in one of the biggest flowing water reservoirs in the world – the Kuybyshev Reservoir. Uniqueness of this natural-technical water body with such large area is pre-defined by significant spatiotemporal changes in physical, chemical and biological parameters, specifying quality and ecological condition of aquatic environment. Studies are conducted using materials of full-scale hydro-ecological observations in the reservoir within vegetation period, in 2016. Some simulation exercises were performed on the model. The model is developed based on hydro-thermodynamics equations and empirical dependences of phosphorous limitation of phytoplanktonic community biomass growth, which is implemented in VOLNA authorial software envelope. The calculation was performed on rectangular spatial grid with spacing of 200 m and timed discretization of 1 day. Within full-scale observations, initial information is acquired, model parameters are calibrated and quality of performed calculations is assessed. Simulation modelling of seasonal phytoplankton field dynamics in Kuybyshev reservoir were analysed using 2D-model of phyto-phosphorous system and results were represented. According to calculations data, phytoplankton biomass growth along reservoir length from headstream to Zhigulevsk HPP dam is observed, as well as intense water blooming locations were detected in estuarial areas and shallow-water parts of the reservoir.
Principal characteristics of transformations in hydrological and ecological conditions of minor rivers within the affected area of mining facilities (on the example of the rivers Karagayly and Khudolaz in the Ural river basin)
Authors: Gareev A M , Belan L N , Goryachev V S , Farkhutdinov A M , Baryshev V I , Shevchenko A M , Ostrovskaya Yu V , Gainanshin M F
Published: September 2021

The article reveals the specific features of the influence posed by mining facilities towards morphometric and hydrological characteristics as well as the environmental condition of small rivers. Given the characteristic features of the impact experienced by the environment (incl. water bodies), the article seeks to identify the peculiarities of the influence caused by a large set of industries involved in the extraction of minerals and their primary treatment leading to production of semi-finished products of non-ferrous metallurgy. The objects of investigation cover the rivers Karagayly and Khudolaz, which are located within the upper reaches of the river Ural and are undergoing an excessively high impact caused by the facilities of the latter industry and the housing and public utilities.
Hydrochemistry of the rivers of the Kama basin in the Northern and Middle Urals
Authors: Kazantseva A S , Kadebskaya O I
Published: September 2021

The hydrochemical indicators of four rivers of the Kama basin (Kolva, Sylva, Shakva and Kishertka), flowing in the territory of the Northern and Middle Urals within the Perm region, have been analysed. It is shown that the river waters of both regions are characterized by common feeding conditions. The data of macro- and microelement analysis made it possible to carry out a modern assessment of the quality of river runoff, as well as to carry out a comparative analysis of the hydrochemical parameters of the waters of the surface runoff of two geographical regions.
The role of the Kama river system in regional development
Authors: Balina T A , Nikolaev R S , Stolbov V A , Yu Chekmeneva L
Published: September 2021

The role and functions of the Kama river system as a natural basis for the socio-economic development of Perm Region are considered. The competitive advantages of the Kama region in the context of the development of the transport and logistics system, energy production, fisheries and aquaculture, tourism and recreation are identified. Special attention is paid to the problems of interaction of the leading industries of Perm Region with the Kama river system. The main directions of involvement of the river system in the national economic complex of the region in the new market conditions are shown. The necessity of positioning Kama as a brand of the Perm Region is justified.
Construction of a model of nutrient export from the catchment using GIS-technologies for a transboundary river in Russia and Finland
Authors: Korobchenkova K D , Ershova A A
Published: September 2021

GIS model SWAT to assess the nutrient load on the catchment area of the Gulf of Finland from the transboundary Seleznevka River (Rakkolanjoki) was applied. All stages of the model setup are considered: preparation of initial data, building the SWAT-model, its calibration and scenario calculations. We consider the possibility of using the SWAT-model for managing the quality of water bodies in Russia and the difficulties that arise while building a model for this catchment area.