bluuebunny/crossref_metadata_2025 huggingface dataset:
The Lie symmetry analysis, optimal system and exact solutions of the (2+1)-dimensional variable coefficients integrable coupled Burgers equations
Authors: Jin Meng , Yang Jiajia , Xin Xiangpeng
Published: October 2023

The variable coefficients integrable coupled Burgers equations (vcICBs) are researched by the Lie symmetry analysis method. The infinitesimal generators, commutative relations and adjoint relations are given. Optimal system of vcICBs are studied by Olver’s method. Based on the optimal system, the (2+1)-dimensional vcICB equations are reduced to (1+1)-dimensional equations. Some new exact solutions of vcICB equations are derived. Some kink solutions, breathe wave solutions and soliton solutions are got by utilising

G
′

/

G

-expansion method, Riccati equation method, Tanh-expansion method and Painlevé analysis method. By altering different coefficient functions, many different types of exact solutions can be derived. The effect of the coefficient functions on the solution is analysed. By studying the evolution of the solution with time t, the dynamic behaviors of the solutions are analysed.
Maximum likelihood bolometry for ASDEX upgrade experiments
Authors: Craciunescu Teddy , Peluso Emmanuele , Murari Andrea , Bernert Matthias , Gelfusa Michela , Rossi Riccardo , Spolladore Luca , Wyss Ivan , David Pierre , Henderson Stuart , Fevrier Olivier ,   ASDEX Upgrade Team
Published: October 2023

Bolometry is an essential diagnostic for calculating the power balances and for the understanding of different physical aspects of tokamak experiments. The reconstruction method based on the Maximum Likelihood (ML) principle, developed initially for JET, has been implemented for ASDEX Upgrade. Due to the availability of a limited number of views, the reconstruction problem is mathematically ill-posed. A regularizing procedure, based on the assumption of smoothness along the magnetic surfaces, given by plasma equilibrium, must also be implemented. A new anisotropic smoothing technique, which acts along locally oriented kernels, has been implemented. The performances of the method have been evaluated, in terms of shapes, resolution and of the derived radiated power, and compared with the bolometry method used routinely on ASDEX Upgrade. The specific advantage of the ML reconstruction algorithm consists of the possibility to assess the uncertainties of the reconstruction and to derive confidence intervals in the emitted radiation levels. The importance of this capability is illustrated.
Improvising CODAS method functionalized with grey numbers to improve the performance of PVD titanium carbon nitride (TiCN) thin film coating: a novel approach
Authors: Das Soham , Protim Das Partha , Ghadai Ranjan Kr , Guha Spandan
Published: October 2023

This experimental study focuses on the deposition of TiCN thin film coating onto a bare p-type silicon substrate using physical vapor deposition (PVD) processes, with varying process parameters. The study employed a design of experiment in accordance with the L
16 orthogonal Array, followed by the implementation of the combinative distance-based assessment (CODAS) method functionalized with grey numbers to enhance the performance of the PVD process for the very first time in the film of thin film deposition. The study also conducted various analyses to examine the coating’s properties, including morphological, structural, microstructural, electrochemical, and mechanical properties. According to the result, the morphology of the coating was wavy in nature, with a smooth microstructure and a few agglomerated particles. The structure of the film indicated that TiCN had a single-phase FCC structure, while the mechanical and electrochemical properties improved with higher N2 flow rates. Additionally, the analysis by CODAS method functionalized with grey numbers suggested that substrate to target distance = 50 mm, N2 flow rate = 25 sccm, and bias voltage = −120 V were the most suitable condition for obtaining the best quality of TiCN thin film coating.
Easy preparation of cobalt oxide/copper oxide composites for gas sensing application
Authors: Khan Madiha , Ferlazzo Angelo , Crispi Simona , Hussain Mozaffar , Neri Giovanni
Published: October 2023

This paper describes the preparation of Co3O4/CuO composites with vary CuO contents (Co3O4/CuO = 1.0wt%/0.50–1.0wt%) using a simple sol–gel process. According to SEM analysis, the composite samples exhibit a round-like morphology. XRD analysis revealed the formation of CuxCoyOz mixed oxide nanostructures. The composite materials were tested as thick films in conductometric devices for ammonia gas sensing at the optimal temperature of 150 °C. The response of Co3O4/CuO (1.0wt%/1.0wt%) composite was found much higher compared to pure Co3O4 and CuO NPs, suggesting that a synergic interaction occurs between the two metal oxide components in improving ammonia gas sensing capability. According to the findings reported, the design of Co3O4/CuO composite heterojunctions by the simple sol–gel process adopted might be an effective way to increase gas sensing toward ammonia gas at mild temperature.
Sub-Doppler dichroism as a useful tool in alkali atom hyperfine spectroscopy
Authors: Karami Mohammad , Heydarinasab Zahra , Sarreshtedari Farrokh
Published: October 2023

Analytical modeling of the sub-Doppler dichroic atomic vapor laser lock error signal shows that the slope of this error signal could be of interest for the identification of transitions in alkali atom hyperfine spectroscopy. Among four D1 line transitions of alkali atoms, the slope sign of the sub-Doppler error signal is different only for the case when the Landé g-factor is negative for both the ground and excited states. The analytical model used, which includes all sublevel transitions, shows very good agreement with the experimental spectroscopy results. The use of this technique allows us to accurately characterize hyperfine transitions in alkali atoms without the need for advanced spectroscopic tools.
Optomechanically induced grating in a graphene based nanocavity
Authors: Abdullaeva B S , Alawsi T , Alawadi A , Alsalamy A
Published: October 2023

The optomechanically induced grating (OMIG) in a nanocavity using a bilayer graphene system as the intracavity medium has been proposed. We investigate the effects of different parameters on the Fraunhofer diffraction pattern of the incident probe light. Here, one mirror of the nanocavity is considered coherently driven by the standing wave coupling and probe fields, whereas the second mirror has mechanical oscillation due to the radiation pressure. We consider interaction of bilayer graphene with the optomechanical cavity and show that OMIG can be obtained corresponding to output probe field frequency. Moreover, we find that under specific parametric conditions, most of the probe energy can transfer to the higher orders of the diffraction and only a small portion remains in the zero order.
Universal resources for quantum computing
Authors: Wang Dong-Sheng
Published: October 2023

Unravelling the source of quantum computing power has been a major goal in the field of quantum information science. In recent years, the quantum resource theory (QRT) has been established to characterize various quantum resources, yet their roles in quantum computing tasks still require investigation. The so-called universal quantum computing model (UQCM), e.g. the circuit model, has been the main framework to guide the design of quantum algorithms, creation of real quantum computers etc. In this work, we combine the study of UQCM together with QRT. We find, on one hand, using QRT can provide a resource-theoretic characterization of a UQCM, the relation among models and inspire new ones, and on the other hand, using UQCM offers a framework to apply resources, study relation among these resources and classify them. We develop the theory of universal resources in the setting of UQCM, and find a rich spectrum of UQCMs and the corresponding universal resources. Depending on a hierarchical structure of resource theories, we find models can be classified into families. In this work, we study three natural families of UQCMs in detail: the amplitude family, the quasi-probability family, and the Hamiltonian family. They include some well known models, like the measurement-based model and adiabatic model, and also inspire new models such as the contextual model that we introduce. Each family contains at least a triplet of models, and such a succinct structure of families of UQCMs offers a unifying picture to investigate resources and design models. It also provides a rigorous framework to resolve puzzles, such as the role of entanglement versus interference, and unravel resource-theoretic features of quantum algorithms.
New measuring system for locating firearm projectiles in the human body based on eddy currents and GMI sensors
Authors: Seixas V , Hall Barbosa C , Costa Monteiro E
Published: October 2023

Noninvasive magnetic mapping for locating non-ferromagnetic metallic foreign bodies, such as firearm projectiles, has a promising application for guiding accurate surgical removals. The strategy consists of inducing eddy currents in the metallic object by applying an external alternating magnetic field. A secondary magnetic field generated by the induced currents in the foreign body can be detected by a high-sensitivity transducer. Previously proposed systems presented constraints to the measurement capability of the transducer imposed by the primary magnetic field interference on their sensing elements. Overcoming these limitations, this work proposes a new configuration of the system that decouples the excitation and measuring stages, arranging their elements symmetrically to generate a spatial distribution of the field lines in such a way that adequate magnetic flux density levels are produced in the region of the foreign body, with values nearly not-detectable at the sensor location. Thereby, the secondary field generated by the induced eddy currents can be amplified, allowing the detection of smaller fragments located at greater depth distances from the skin. The measuring system concept, the spatial distribution of the primary and secondary magnetic fields, and the new approach’s performance to localize foreign bodies are presented.
Metrological perspective on the use of ultrasound physiotherapy equipment in Brazil
Authors: Silva J G D , Alvarenga A V , Costa-Félix R P B
Published: October 2023

Despite several scientific proofs about the success of using therapeutic ultrasound for different therapies, there are also reports of failures and ineffectiveness in applied treatments. Much of this failure is due to the poor working conditions of the ETUS equipment used, which causes the reduction or absence of therapeutic effects. This survey asked professionals about the methods they use and the methods they know and are available on the market to test their equipment through a questionnaire. This study aimed to discuss, for the metrological perspective, the use of ultrasound physiotherapy equipment in Brazil. A problem for the metrological reliability of ETUS is related to the lack of metrological culture among users, who do not adopt procedures to assess their equipment, often because they are unaware of its importance and need. Periodic checks on equipment would give physiotherapists a resource with greater reliability and possibly more efficient therapies.
Polymer blocks homogeneity concerning the speed of sound for in vitro studies in implant dentistry
Authors: Morais G C , Mayworm R C , Giosa D T , Fontão F N G K , Granjeiro J M , Costa-Felix R P B
Published: October 2023

Dentistry implants methods are recursively enhancing the image localisation approach to improve patient point of intercession accuracy. Previous planning of the surgical act is on the cut edge of the technology. Materials that mimic the implant house, i.e., the maxillary bone, have been developed and improved material technology. Standard non-invasive and non-ionising radiation technologies are relevant tools to that approach. Ultrasound imaging techniques play a prominent role in that matter. Nevertheless, recent polymer materials specially developed to help the pre-implant studies had not been evaluated about their homogeneity of ultrasound parameters. Two specially developed polymer materials have their speed of sound analysed in a metrologically based methodology. At 1 MHz, a set of 10 blocks were considered statistically equivalent, unless one specimen. The speed of sound was 1020 m s−1 (expanded uncertainty for p = 0.95 equals 22 m s−1) and 1676 m s−1 (U0.95 = 10 m s−1). The ultrasound homogeneity is a vital outcome of the reliability of those materials used in dentistry implant pre-clinical studies.
Detection of Microbiological Contamination in Cell Cultures and their Raw Materials: a 6 years report of this activity.
Authors: Ramos-Junior J L P , Monteiro O S , dos Santos N C , Correa R , Cavalcanti D P , Martins J , Boldrini L , Granjeiro J M , Folgueras-Flatschart A V
Published: October 2023

Contaminations in cell cultures are a source of concern for biotechnology laboratories, bio products manufacturers and cell banks as they involve economical loss, time loss and non-valid results. The main issues are fungi, bacteria (including mycoplasmas) and viruses. In this study, we present a retrospective of cell cultures quality control and their raw materials carried out at INMETRO throughout 6 years. From 2014 to 2019, different cell lines and raw materials derived from LABIO, from partner institutions of research projects, or from cooperation agreements were assessed. The detection of mycoplasmas were made using the biochemical method MycoAlert Plus. Contamination by bacteria and fungi were detected by a microbiological culturing according to the Brazilian Pharmacopoeia. Among the 944 assays carried out to detect bacteria and fungi; 5.6% presented contamination. Among 1143 assays of mycoplasmas detection; 10.8% presented contamination. Regarding raw materials assessment, 0.7% and 7.7% were contaminated with mycoplasmas and bacteria/fungi, respectively. In total, 8% of all samples presented contamination: 5.6% by mycoplasmas, 2.4% by bacteria/fungi and 0.1% by both. The dissemination of Good Practices on Cells Culture, the availability of these assays and the support of the implementation given to laboratories which are interested have been our contribution to improve control quality in the activity of cell cultures.
Convolutional Neural Network for non-invasive magnetic foreign body localization in the human body
Authors: Rogozinski M , Barbosa C R H , Costa Monteiro E
Published: October 2023

Ferromagnetic foreign bodies accidentally inserted in patients usually need to be surgically removed. Their location can be estimated by measuring the magnetic field generated by the object and solving the magnetic inverse problem to locate the source based on the magnetic field maps configuration. Considering ferromagnetic straight needles (hypodermic or sewing, for example) and a computer simulation of the magnetic flux density based on Biot-Savart’s Law, this paper presents an algorithm based on Convolutional Neural Networks (CNN) to find the depth, the angles of inclination and rotation and the center of the needle inside the human body. The proposed model presents low RMSE values and type A measurement uncertainty for the depth, the inclination angle, the rotation angle, and for the displacement Δ between the midpoint of the distance connecting the magnetic field extreme values and the foreign body center, all of which adequate for use in therapeutic procedures.
Characterization of an OCT probe for use in the diagnosis of precancerous lesions of the cervix
Authors: Cordes A H , Couceiro I B , Alvarenga A D , Malinovski I , de Andrade C V , Russomano F B , von der Weid J P
Published: October 2023

The development of an auxiliary diagnostic tool (OCT probe) for application in the assessment of cervical cancer is being carried out and may have an impact on the diagnostic process and, consequently, on the reduction of the incidence of female mortality from cervical cancer, by allowing a more accurate assessment of the extent of the lesion and by enabling the expansion of this assessment within the endocervical canal. In addition to the scientific result, the use of available equipment will boost the quality of clinical care currently available for diagnosis. Combining technical development with a precise methodology and clinical application, the probe developed will have a scientific impact of socio-economic relevance for society. As it is an optical measurement, it is necessary to evaluate the optical characteristics of the developed probes and the choice of one of them was made taking into account the measurements carried out and the application of metrological concepts.
A simple Kibble balance approach for principle demonstration at Inmetro
Authors: Cacais F L , Loayza V M , Beatrici A , Quintão D , Rebelo A S
Published: October 2023

This work shows the results obtained by Inmetro’s mass lab implementation of a simple Kibble balance approach for demonstration of its mass measurement principle based on the Planck’s constant. It is based on some modifications of Mimimal Watt Balance work reducing the required electrical measurements by using two loudspeakers mechanically coupled so that one of them acts as a linear actuator in order to perform BL measurements in the moving phase. The mean BL value obtained in weighing phase was 2.66 N/A and in moving phase 2.67 N/A. The maximum error of mass values measured for standard weights in the range from 5 g to 50 g was lower than 5%.
A reference system to calibrate low-current meters in the range of picoamperes to microamperes
Authors: Pinto M V V , Ventura R V F , Landim R P , David R P
Published: October 2023

The calibration of low current meters in the range of picoamperes up to microamperes is important for the electronics industry, for the photometry area, and especially for the ionizing radiation area. In Brazil, traceability is limited to ten microamperes. In this paper, a reference system using Ohm’s law method is presented. It was possible to calibrate an electrometer between 2 picoamperes and 20 microamperes, with uncertainties between 0.70 % and 0.000060 %, respectively, as well as to validate the developed system and Ohm’s law method by comparing it with the method used to calibrate values above 10 microamperes, in an intralaboratory comparison.
Identification and evaluation of uncertainty contributions to optical current sensor measurement uncertainty
Authors: Costa M M , Costa J C W A
Published: October 2023

Optical current sensors can replace traditional current sensor due to their several advantages, as electromagnetic immunity, low dimensions, low cost and others. One of the current main challenges is to develop optical current sensors with good accuracy and stability. This paper presents identification and evaluation of uncertainty contributions to measurement uncertainty evaluation of optical current sensors based on Faraday effect.
Quality infrastructure for energy efficiency of household appliances in Latin America and the Caribbean
Authors: Kyriazis G A , Göthner K-C
Published: October 2023

The main activities and results of the energy efficiency component of the regional project ‘Quality Infrastructure for Renewable Energy and Energy Efficiency in Latin America and the Caribbean’ are presented. This project was implemented by the Organization of American States (OAS), the Inter-American System of Metrology (SIM), the Pan American Standards Commission (COPANT), the Inter-American Accreditation Cooperation (IAAC), and the Physikalisch-Technische Bundesantalt (PTB). The main objective of its energy efficiency component consisted in improving the regional quality infrastructure for energy efficiency of household appliances.
Uncertainty assessment of a resistive voltage divider for binary step-up method implementation in HVDC applications
Authors: Vitorio P C de O , de Souza L A A , Landim R P , do Prado C B
Published: October 2023

The most used methods for determining the ratio of High Voltage Direct Current (HVDC) standard resistive dividers are described in this paper. The binary step-up method was chosen to metrologically characterize a HVDC resistive divider, in order to achieve local traceability to the SI from Josephson Voltage Standards. A Monte Carlo-based simulation was performed to estimate the uncertainty levels of each step from 1.25 kV up to 10 kV, considering that the main components are the uncertainty of the digital multimeter and the voltage source. It was found a variation up to 64-fold in the standard deviation of the voltage output, for a uniform distribution, when the voltage source uncertainty was increased up to 10-fold.
Paving the road towards ITER relevant long deuterium pulses at ELISE by investigating improved operational scenarios
Authors: Wünderlich D. , Yordanov D. , Riedl R. , Heinemann B. , Fantz U.
Published: October 2023

Hydrogen plasma pulses of 1000 s with an extracted current density of over 90 % of the ITER target value (while also fulfilling the requirements for the electron-ion ratio and the global top/bottom beam homogeneity) were demonstrated at the ELISE test facility with its half ITER-size negative hydrogen ion source in pulsed extraction mode, i.e. short beam extraction phases of ≈10 s each ≈150 s, and using the so-called potential rods. In deuterium roughly 67 % of the ITER target for the extracted current density has been achieved for pulses longer than 45 minutes, limited by a pronounced vertical asymmetry and increase with time
in
the co-extracted electron current.

In order to stabilize the co-extracted electron current during long pulses, particularly in deuterium, improved operational scenarios have to be developed. At ELISE, it was investigated the possibility to remove the potential rods and instead to set the bias plate to a positive voltage with respect to the source vessel. In this operational scenario short pulses in deuterium can be achieved with an extracted negative ion current density of up to 90 % of the ITER target value.

In order to improve the physics insight, a 2D fluid code is applied. The first general result is that the modified potentials of surfaces close to the extraction system strongly affect the fluxes of charged particles towards different surfaces and consequently can result in a reduction of the co-extracted electron current.

The temporal behaviour during long pulses with pulsed extraction, in particular of the co-extracted electrons, demonstrates a significant impact of the beam extraction on the caesium dynamics. Thus, CW extraction is mandatory for developing fully ITER relevant operational scenarios. After an extensive upgrade, ELISE is now capable of performing CW pulses, i.e. long-pulse beam extraction.
The latest developments of microwave diagnostics for high temperature plasma in ELVA-1 company
Authors: Korneev D. , Petrov S. , Markov S.
Published: October 2023

For nearly 30 years, we have been designing and supplying instruments for microwave diagnostics of high temperature plasma. This report provides a description of the mm-wave components we utilize to make diagnostics within the frequency range of 26–330 GHz. While most of these components are standard and readily available on the market, we have also developed a few specific devices that simplify the architecture of our instruments. The article includes descriptions of these devices: Backward Wave Oscillators (BWO), Impact Ionization Avalanche Transit-Time diode (IMPATT) sources, IMPATT Active Frequency Multipliers (AFM), Noise Sources, and Electronically Controlled Attenuators. Furthermore, we offer an overview of the microwave plasma diagnostics we have supplied, including ECE radiometers operating at 50–220 GHz, as well as heterodyne interferometers operating at fixed frequency 94 GHz, 140 GHz, or 300 GHz. We also discuss methods employed to ensure measurement stability and present the achieved results. The advent of the new era of modern Monolithic Microwave Integrated Circuit (MMIC) based devices has brought forth exciting possibilities. As an example, we discuss the upgrade of the low noise receiver for the Collective Thomson Scattering (CTS) diagnostic at Wendelstein 7-X, which enables ion temperature measurements in the plasma core [1]. Lastly, we provide a list of MMIC-based devices that are currently available and have garnered the attention of the plasma diagnostics community.
Solid-state Marx generator based on saturable pulse transformer and fast recovery diodes
Authors: Zhuang Longyu , Zhu Kai , Rao Junfeng , Zhuang Jie
Published: October 2023

Solid-state compact Marx generator using saturable pulse
transformer (SPT) and fast recovery diodes has been proposed. The
primary circuit is switched by three MOSFETs connected in
parallel. The SPT functions as a step-up transformer to increase the
voltage amplitude and as a closing switch for the secondary
circuit. Meanwhile, all the SPTs share the same magnetic core to
achieve a compact structure and ensure good synchronization. The
energy storage capacitors on the secondary sides are charged through
the unsaturated SPT. When the SPT saturates, the capacitors firstly
transfer a little energy to the saturated inductors through the
diodes reversely during their reverse recovery process. Currents
rise quickly in these inductors until diodes totally recover to
reverse blocking state. Then capacitors discharge in series to the
load and high-voltage pulses are generated over the load. With the
currents in the saturated inductors, the front edges of pulses are
no longer affected by them but are dominated the turn-off speed of
the diodes, which makes high-voltage and high-current pulses with
short front edges possible. The regular and cheap fast recovery
diodes in the generator act as semiconductor opening switch to
sharpen the pulse front edges. Experiments were carried out with a
4-stage Marx generator prototype, 10.8-kV high-voltage pulses with a
front edge of 11 ns, a pulse width of 190 ns, were obtained over a
100-Ω resistive load. The total energy efficiency is
49.8%. The proposed Marx generator using regular fast recovery
diodes is compact, cheap, and efficient to generate high-voltage
pulses with short front edges.
Fast spacecraft charging induced by a high-power electron beam emission and its mitigation through a plasma contactor
Authors: Xue Bixi , Zhao Qiang , Zhang Fang , Dong Zhiwei , Hao Jianhong , Fan Jieqing , Cao Xiangchun
Published: October 2023

Active sounding experiments, including tracing magnetic field lines and magnetospheric sounding, may be accomplished in the GEO environment by the active emission of high-power electron beams. The continual emission of electron beam pulses during such experiments may result in the accumulation of positive charges on the spacecraft surface and a rise in the spacecraft potential, which might prohibit the normal emission of succeeding pulses. The plasma contactor has been shown to be a reliable method for neutralizing the spacecraft potential. But as the active charging effect brought on by the high-current electron beam manifests itself more quickly, it is still unknown whether the plasma contactor can reliably control the spacecraft potential in this circumstance. In this study, a two-dimensional PIC model is used to examine the active charging effect brought on by high-power electron beam emission. Findings indicate that the potential neutralization process may be affected by the ion sheath that forms close to the emitting surface of the plasma contactor, which cuts the electrical connection between the spacecraft and plasma in space. By evaluating the quantities and growth speeds of different particles during active charging, we discover that lowering the particle density or pre-emission time of the plasma contactor may bring the spacecraft potential to the equilibrium state. Additionally, the high-current electron beam raises the peak potential, making it more difficult to launch the electron beam properly before the spacecraft potential reaches equilibrium. In contrast, the high-energy electron beam is less susceptible to the active charging effect.
Improvement of miniaturized 2.45 GHz ECR plasma flood gun at PKU
Authors: Cui Bujian , Peng Shixiang , Wu Wenbin , Ma Tenghao , Jiang Yaoxiang , Guo Zhiyu , Chen Jiaer
Published: October 2023

In an ion implanter, plasma flood gun (PFG) is used to
provide electrons to neutralize the accumulated charge on the wafer
surface to avoid breakdown damage. With the development of ion
implantation technology, four key requirements have been put forward
for PFG. They are simple structure, plasma with high density and low
electron temperature, no metal contamination and long life. The
existing PFG, such as the filament type PFG, can hardly meet the
above requirements at the same time. 2.45 GHz ECR ion source with
the advantages of high beam density, high stability, long life time
and no filament metal contamination, has shown great potential to
work as PFG. Recently, a miniaturized 2.45 GHz permanent magnet
electron cyclotron resonance PFG (PMECR-PFG) has been developed at
Peking University (PKU). In our previous test, 8.8 mA electron
extraction current was obtained with argon gas. In this work, by
optimizing the magnetic field configuration to a resonant
configuration, the performance of this ECR-PFG was greatly
improved. With 100 W microwave power, an 80 mA electron current
load was obtained under the extraction voltage of 0.1 kV. To
minimize the metal contamination, a three-slit graphite plasma
electrode was fabricated and a 50 mA load was generated at only
30 W RF power. During all tests, the gas consumption rate is lower
than 0.6 sccm, which is beneficial to maintain the vacuum of
implanter beamline.
Direct Poisson neural networks: learning non-symplectic mechanical systems
Authors: Šípka Martin , Pavelka Michal , Esen Oğul , Grmela Miroslav
Published: October 2023

In this paper, we present neural networks learning mechanical systems that are both symplectic (for instance particle mechanics) and non-symplectic (for instance rotating rigid body). Mechanical systems have Hamiltonian evolution, which consists of two building blocks: a Poisson bracket and an energy functional. We feed a set of snapshots of a Hamiltonian system to our neural network models which then find both the two building blocks. In particular, the models distinguish between symplectic systems (with non-degenerate Poisson brackets) and non-symplectic systems (degenerate brackets). In contrast with earlier works, our approach does not assume any further a priori information about the dynamics except its Hamiltonianity, and it returns Poisson brackets that satisfy Jacobi identity. Finally, the models indicate whether a system of equations is Hamiltonian or not.
Coagulation equations with source leading to anomalous self-similarity
Authors: Ferreira M A , Franco E , Lukkarinen J , Nota A , Velázquez J J L
Published: October 2023

We study the long-time behaviour of the solutions to Smoluchowski coagulation equations with a source term of small clusters. The source drives the system out-of-equilibrium, leading to a rich range of different possible long-time behaviours, including anomalous self-similarity. The coagulation kernel is non-gelling, homogeneous, with homogeneity

γ
⩽
−
1

, and behaves like

x

γ
+
λ

y

−
λ

when

y
≪
x

with

γ
+
2
λ
>
1

. Our analysis shows that the long-time behaviour of the solutions depends on the parameters γ and λ. More precisely, we argue that the long-time behaviour is self-similar, although the scaling of the self-similar solutions depends on the sign of

γ
+
λ

and on whether

γ
=
−
1

or

γ
<
−
1

. In all these cases, the scaling differs from the usual one that has been previously obtained when

γ
+
2
λ
<
1

or

γ
+
2
λ
⩾
1
,
γ
>
−
1

. In the last part of the paper, we present some conjectures supporting the self-similar ansatz also for the critical case

γ
+
2
λ
=
1
,
γ
⩽
−
1

.
Differences in cell shape, motility, and growth reflect chromosomal number variations that can be visualized with live-cell ChReporters
Authors: Tobin Michael P. , Pfeifer Charlotte R. , Zhu Peter Kuangzheng , Hayes Brandon H. , Wang Mai , Vashisth Manasvita , Xia Yuntao , Phan Steven H. , Belt Susanna A. , Irianto Jerome , Discher Dennis E.
Published: October 2023

Chromosome numbers often change dynamically in tumors and cultured cells, which complicates therapy as well as understanding genotype-mechanotype relationships. Here we use a live-cell “ChReporter” method to identify cells with a single chromosomal loss in efforts to better understand differences in cell shape, motility, and growth. We focus on a standard cancer line and first show clonal populations that retain the ChReporter exhibit large differences in cell and nuclear morphology as well as motility. Phenotype metrics follow simple rules, including migratory persistence scaling with speed, and cytoskeletal differences are evident from drug responses, imaging, and single-cell RNA sequencing. However, mechanotype–genotype relationships between fluorescent ChReporter-positive clones proved complex and motivated comparisons of clones that differ only in loss or retention of a Chromosome-5 ChReporter. When lost, fluorescence-null cells show low expression of Chromosome-5 genes, including a key tumor suppressor APC that regulates microtubules and proliferation. Colonies are compact, nuclei are rounded, and cells proliferate more, with drug results implicating APC, and patient survival data indicating an association in multiple tumor-types. Visual identification of genotype with ChReporters can thus help clarify mechanotype and mechano-evolution.
C-banding characterization of centric fusion and heterochromatin polymorphisms in the water-hyacinth grasshopper, Cornops aquaticum (Orthoptera: Acrididae)
Authors: Colombo Pablo , Bressa María José , Remis María Isabel
Published: October 2023

The water-hyacinth grasshopper, Cornops aquaticum (Orthoptera: Acrididae), shows a clinal variation for 3 Robertsonian translocation (centric fusion) polymorphisms in the southern extreme of its wide geographical distribution. It is a Neotropical semiaquatic grasshopper that lives, feeds, and lays eggs exclusively on floating plants of the family Pontederiaceae, or water-hyacinths, between 23° N (Southern Mexico) and 35° S (Central Argentina and Uruguay). Given the invasive-species status of Pontederia (formerly Eichhornia) crassipes and the voraciousness of these grasshoppers, they were considered as a potential biological control agent in addition to other natural enemies. We already described the association of the rearrangements with geographical and climatic variables, phenotypic variation, trivalent orientation, effects on recombination, and relationship with microsatellite variability. Here we analyze the distribution of constitutive heterochromatin in 2 populations of C. aquaticum in order to (i) provide consistent markers for a better distinction between all chromosomes, those which are involved in the centric fusions, and those which are not, and (ii) describe possible polymorphisms for C-positive supernumerary segments, given that, on conventional staining analysis, it was frequent to find heteromorphic autosomal bivalents. The cytogenetic analysis allowed us to get a detailed characterization of the constitutive heterochromatin distribution, providing unmistakable chromosome markers of the large, fusion-bearing chromosomes as well as the C-positive, polymorphic supernumerary segments.
The Capability Approach and the WHO healthy ageing framework (for the UN Decade of Healthy Ageing)
Authors: Venkatapuram Sridhar , Amuthavalli Thiyagarajan Jotheeswaran
Published: October 2023

This commentary discusses the WHO definition of health ageing in terms of functional abilities, and the problem definition and evidence-based public health response framework outlined in the 2015 WHO Report on Ageing and Health. After identifying the neglect of older people in health policy at national and global levels, some data are presented on the majority of COVID-19 deaths being older people. The discussion then focuses on the underlying ethical and analytical framework of functional abilities provided by the Capability Approach. The approach is presented as distinguishing between achievement and capability, the ethical significance of recognising both, and its inclusion of surrounding social conditions from local to global in assessing wellbeing of older people’s functional abilities. Measurement of functional abilities, informed by the Capabilities Approach, is stated to be an enormous and crucial task in establishing a global baseline, and making progress in improving the health and wellbeing of older people.
Breaking the barriers of data scarcity in drug–target affinity prediction
Authors: Pei Qizhi , Wu Lijun , Zhu Jinhua , Xia Yingce , Xie Shufang , Qin Tao , Liu Haiguang , Liu Tie-Yan , Yan Rui
Published: October 2023

Accurate prediction of drug–target affinity (DTA) is of vital importance in early-stage drug discovery, facilitating the identification of drugs that can effectively interact with specific targets and regulate their activities. While wet experiments remain the most reliable method, they are time-consuming and resource-intensive, resulting in limited data availability that poses challenges for deep learning approaches. Existing methods have primarily focused on developing techniques based on the available DTA data, without adequately addressing the data scarcity issue. To overcome this challenge, we present the Semi-Supervised Multi-task training (SSM) framework for DTA prediction, which incorporates three simple yet highly effective strategies: (1) A multi-task training approach that combines DTA prediction with masked language modeling using paired drug–target data. (2) A semi-supervised training method that leverages large-scale unpaired molecules and proteins to enhance drug and target representations. This approach differs from previous methods that only employed molecules or proteins in pre-training. (3) The integration of a lightweight cross-attention module to improve the interaction between drugs and targets, further enhancing prediction accuracy. Through extensive experiments on benchmark datasets such as BindingDB, DAVIS and KIBA, we demonstrate the superior performance of our framework. Additionally, we conduct case studies on specific drug–target binding activities, virtual screening experiments, drug feature visualizations and real-world applications, all of which showcase the significant potential of our work. In conclusion, our proposed SSM-DTA framework addresses the data limitation challenge in DTA prediction and yields promising results, paving the way for more efficient and accurate drug discovery processes.
The progranulin cleavage product granulin 3 exerts a dominant negative effect on animal fitness
Authors: Wang Austin L , Mambou Edwina A , Kao Aimee W
Published: October 2023

Progranulin is an evolutionarily conserved protein that has been implicated in human neurodevelopmental and neurodegenerative diseases. Human progranulin is comprised of multiple cysteine-rich, biologically active granulin peptides. Granulin peptides accumulate with age and stress, however their functional contributions relative to full-length progranulin remain unclear. To address this, we generated C. elegans strains that produced quantifiable levels of both full-length progranulin/PGRN-1 protein and cleaved granulin peptide. Using these strains, we demonstrated that even in the presence of intact PGRN-1, granulin peptides suppressed the activity of the lysosomal aspartyl protease activity, ASP-3/CTSD. Granulin peptides were also dominant over PGRN-1 in compromising animal fitness as measured by progress through development and stress response. Finally, the degradation of human TDP-43 was impaired when the granulin to PGRN-1 ratio was increased, representing a disease-relevant downstream impact of impaired lysosomal function. In summary, these studies suggest that not only absolute progranulin levels, but also the balance between full-length progranulin and its cleavage products, is important in regulating lysosomal biology. Given its relevance in human disease, this suggests that the processing of progranulin into granulins should be considered as part of disease pathobiology and may represent a site of therapeutic intervention.
A large-scale microRNA transcriptome-wide association study identifies two susceptibility microRNAs, miR-1307-5p and miR-192-3p, for colorectal cancer risk
Authors: Chen Zhishan , Lin Weiqiang , Cai Qiuyin , Kweon Sun-Seog , Shu Xiao-Ou , Tanikawa Chizu , Jia Wei-Hua , Wang Ying , Su Xinwan , Yuan Yuan , Wen Wanqing , Kim Jeongseon , Shin Aesun , Jee Sun Ha , Matsuo Keitaro , Kim Dong-Hyun , Wang Nan , Ping Jie , Shin Min-Ho , Ren Zefang , Oh Jae Hwan , Oze Isao , Ahn Yoon-Ok , Jung Keum Ji , Gao Yu-Tang , Pan Zhi-Zhong , Kamatani Yoichiro , Han Weidong , Long Jirong , Matsuda Koichi , Zheng Wei , Guo Xingyi
Published: October 2023

Transcriptome-wide association studies (TWAS) have identified many putative susceptibility genes for colorectal cancer (CRC) risk. However, susceptibility miRNAs, critical dysregulators of gene expression, remain unexplored. We genotyped DNA samples from 313 CRC East Asian patients and performed small RNA sequencing in their normal colon tissues distant from tumors to build genetic models for predicting miRNA expression. We applied these models and data from genome-wide association studies (GWAS) including 23 942 cases and 217 267 controls of East Asian ancestry to investigate associations of predicted miRNA expression with CRC risk. Perturbation experiments separately by promoting and inhibiting miRNAs expressions and further in vitro assays in both SW480 and HCT116 cells were conducted. At a Bonferroni-corrected threshold of P < 4.5 × 10−4, we identified two putative susceptibility miRNAs, miR-1307-5p and miR-192-3p, located in regions more than 500 kb away from any GWAS-identified risk variants in CRC. We observed that a high predicted expression of miR-1307-5p was associated with increased CRC risk, while a low predicted expression of miR-192-3p was associated with increased CRC risk. Our experimental results further provide strong evidence of their susceptible roles by showing that miR-1307-5p and miR-192-3p play a regulatory role, respectively, in promoting and inhibiting CRC cell proliferation, migration, and invasion, which was consistently observed in both SW480 and HCT116 cells. Our study provides additional insights into the biological mechanisms underlying CRC development.
Convergent evolving finite element approximations of boundary evolution under shape gradient flow
Authors: Gong Wei , Li Buyang , Rao Qiqi
Published: October 2023

As a specific type of shape gradient descent algorithm, shape gradient flow is widely used for shape optimization problems constrained by partial differential equations. In this approach, the constraint partial differential equations could be solved by finite element methods on a domain with a solution-driven evolving boundary. Rigorous analysis for the stability and convergence of such finite element approximations is still missing from the literature due to the complex nonlinear dependence of the boundary evolution on the solution. In this article, rigorous analysis of numerical approximations to the evolution of the boundary in a prototypical shape gradient flow is addressed. First-order convergence in time and $k$th order convergence in space for finite elements of degree $k\geqslant 2$ are proved for a linearly semi-implicit evolving finite element algorithm up to a given time. The theoretical analysis is consistent with the numerical experiments, which also illustrate the effectiveness of the proposed method in simulating two- and three-dimensional boundary evolution under shape gradient flow. The extension of the formulation, algorithm and analysis to more general shape density functions and constraint partial differential equations is also discussed.
Post-processing and improved error estimates of numerical methods for evolutionary systems
Authors: Franz Sebastian
Published: October 2023

We consider evolutionary systems, i.e., systems of linear partial differential equations arising from the mathematical physics. For these systems, there exists a general solution theory in exponentially weighted spaces, which can be exploited in the analysis of numerical methods. The numerical method considered in this paper is a discontinuous Galerkin method in time combined with a conforming Galerkin method in space. Building on our recent paper (Franz, S., Trostorff, S. & Waurick, M. (2019) Numerical methods for changing type systems. IMAJNA, 39, 1009–1038), we improve some of the results, study the dependence of the numerical solution on the weight parameter and consider a reformulation and post-processing of its numerical solution. As a by-product, we provide error estimates for the dG-C0 method. Numerical simulations support the theoretical findings.
Inpatient nurses’ preferences and decisions with risk information visualization
Authors: Jeffery Alvin D , Reale Carrie , Faiman Janelle , Borkowski Vera , Beebe Russ , Matheny Michael E , Anders Shilo
Published: October 2023

Objective

We examined the influence of 4 different risk information formats on inpatient nurses’ preferences and decisions with an acute clinical deterioration decision-support system.

Materials and methods

We conducted a comparative usability evaluation in which participants provided responses to multiple user interface options in a simulated setting. We collected qualitative data using think aloud methods. We collected quantitative data by asking participants which action they would perform after each time point in 3 different patient scenarios.

Results

More participants (n = 6) preferred the probability format over relative risk ratios (n = 2), absolute differences (n = 2), and number of persons out of 100 (n = 0). Participants liked average lines, having a trend graph to supplement the risk estimate, and consistent colors between trend graphs and possible actions. Participants did not like too much text information or the presence of confidence intervals. From a decision-making perspective, use of the probability format was associated with greater concordance in actions taken by participants compared to the other 3 risk information formats.

Discussion

By focusing on nurses’ preferences and decisions with several risk information display formats and collecting both qualitative and quantitative data, we have provided meaningful insights for the design of clinical decision-support systems containing complex quantitative information.

Conclusion

This study adds to our knowledge of presenting risk information to nurses within clinical decision-support systems. We encourage those developing risk-based systems for inpatient nurses to consider expressing risk in a probability format and include a graph (with average line) to display the patient’s recent trends.