bluuebunny/crossref_metadata_2025 huggingface dataset:
Enrichment of microplastic pollution by micro-nanobubbles
Authors: Wang Jing , Wang Zihan , Pei Fangyuan , Wang Xingya
Published: March 2022

Microplastic pollution has become a global environmental concern. It has been reported that microplastics are easily accessible to a wide range of aquatic organisms and ultimately enter the human body along the food chain. They pose a severe threat to ecosystems, organisms and even human health due to their durability and persistence. However, how to reduce microplastic pollution still remains a challenge in terms of scientific techniques and policy-making. There is currently still a lack of effective methods for microplastic recycling and removal. Luckily, a new technique, micro-nanobubbles (MNBs), may provide a possible and highly effective method to enrich microplastic pollution: their great advantages[1] include a high specific surface area, long lifetime and ability to adsorb microplastics of the same size and hydrophobicity. Then they further adsorb on larger bubbles such as microbubbles or millimeter bubbles and float to the water surface together. In this study, we present a new method using MNBs to enrich microplastic pollution with high efficiency. Two types of microplastics, millimeter-scale plastic fragments and microplastic particles, were chosen as the model microplastic pollution systems to study the enrichment efficiency of MNBs on microplastics. Results showed that MNBs can efficiently enrich these microplastics. The enrichment efficiency increases with flotation time until a maximum value is reached. It is proved that MNBs not only collect the microplastic pollution but also reduce detergent use in domestic laundry sewage. This is because detergent, as a surfactant, is easily absorbed on the surface of MNBs and can be collected together with the microplastic pollution. Our research has demonstrated that the MNB technique could be promising for use in microplastic recycling and reducing detergent pollution in daily life.
Improved phenomenological nuclear charge radius formulae with kernel ridge regression *
Authors: Ma Jian-Qin , Zhang Zhen-Hua
Published: March 2022

The kernel ridge regression (KRR) method with a Gaussian kernel is used to improve the description of the nuclear charge radius by several phenomenological formulae. The widely used

,

and

formulae, and their improved versions including isospin dependence, are adopted as examples. The parameters in these six formulae are refitted using the Levenberg–Marquardt method, which give better results than the previous versions. The radius for each nucleus is predicted with the KRR network, which is trained with the deviations between experimental and calculated nuclear charge radii. For each formula, the resultant root-mean-square deviations of 884 nuclei with proton number

and neutron number

can be reduced to about 0.017 fm after considering the modification by the KRR method. The extrapolation ability of the KRR method for the neutron-rich region is examined carefully and compared with the radial basis function method. It is found that the improved nuclear charge radius formulae using the KRR method can avoid the risk of overfitting, and have a good extrapolation ability. The influence of the ridge penalty term on the extrapolation ability of the KRR method is also discussed. Finally, the nuclear charge radii of several recently observed K and Ca isotopes are analyzed.
Neural decoding of semantic concepts: a systematic literature review
Authors: Rybář Milan , Daly Ian
Published: March 2022

Objective. Semantic concepts are coherent entities within our minds. They underpin our thought processes and are a part of the basis for our understanding of the world. Modern neuroscience research is increasingly exploring how individual semantic concepts are encoded within our brains and a number of studies are beginning to reveal key patterns of neural activity that underpin specific concepts. Building upon this basic understanding of the process of semantic neural encoding, neural engineers are beginning to explore tools and methods for semantic decoding: identifying which semantic concepts an individual is focused on at a given moment in time from recordings of their neural activity. In this paper we review the current literature on semantic neural decoding. Approach. We conducted this review according to the Preferred Reporting Items for Systematic reviews and Meta-Analysis (PRISMA) guidelines. Specifically, we assess the eligibility of published peer-reviewed reports via a search of PubMed and Google Scholar. We identify a total of 74 studies in which semantic neural decoding is used to attempt to identify individual semantic concepts from neural activity. Main results. Our review reveals how modern neuroscientific tools have been developed to allow decoding of individual concepts from a range of neuroimaging modalities. We discuss specific neuroimaging methods, experimental designs, and machine learning pipelines that are employed to aid the decoding of semantic concepts. We quantify the efficacy of semantic decoders by measuring information transfer rates. We also discuss current challenges presented by this research area and present some possible solutions. Finally, we discuss some possible emerging and speculative future directions for this research area. Significance. Semantic decoding is a rapidly growing area of research. However, despite its increasingly widespread popularity and use in neuroscientific research this is the first literature review focusing on this topic across neuroimaging modalities and with a focus on quantifying the efficacy of semantic decoders.
The effect of extraction time on the quality of brown seaweed Na-Alginate Sargassum polycisteum as the base material for SBK Edible Film
Authors: Latifah R N , Rahmania S , Rohmah B L
Published: March 2022

Brown seaweed is an alginate-producing seaweed because of its high polysaccharide hydrocolloid content. Alginate is one type of hydrocolloid by organic polymers in water. This study aimed to obtain a suitable method in producing sodium alginate to produce a large yield. The research method includes the preparation of seaweed, extraction, and purification of alginate using EDTA, and testing the quality of the resulting alginate. The results showed that the yield of alginate produced in this study was 18.47-24.31%. The viscosity and water content test results showed that the alginate yield was 892 cps with an extraction time of 6 hours and 14.82% (w/v). Functional group analysis revealed a mannonate fingerprint region that indicated the absorption peak from alginate characteristics. The ash content test produced is in the range of 14.25%-26.57%. The pH of Na-alginate is in the range between 8-10. Water vapor transmission rate is ranged from 10.13-11.56 g/m2.hours to edible film application.
Study of mixed binding agent La-MOF and chelex-100 by diffusive gradient in thin films (DGT) devices
Authors: Julianti S , Saefumillah A , Zulys A
Published: March 2022

The release of phosphor in the form of high phosphate from sediments to the aquatic system triggers a eutrophication process. It occurs due to the influence of the iron redox system where phosphate bound to iron(III) oxyhydroxide is reduced to iron(II) which will be released into aquatic systems under anoxic conditions. Therefore, developing an in-situ technique to measure the release of phosphor and iron simultaneously contributes to a better analysis. The method uses Lanthanum MOF, a porous material with a high surface area to bind labile phosphate species and Chelex-100 and bind iron(II) ions in Diffusive Gradient in Thin Films (DGT). The largest value of CDGT/Csolution for Iron(II) ion was 1.12, and for the labile phosphate species, the maximum value was 1.39 within 24 hours. Tests on variations in the pH solution obtained optimum results for Iron(II) ions, namely at pH 2.5 - 4.5. Meanwhile, the labile phosphate species produced the optimum result at a pH of 2.5-8.6. This study shows that the ability of the binding agent combination in the DGT tool to bind Iron(II) ions and labile phosphate species depends on the immersion (soaking) time and pH.
Atmospheric pressure plasma jet for surface material modification: a mini-review
Authors: Setiawan U H , Nurcahyo I F , Saraswati T E
Published: March 2022

Plasma jet is one of the methods for surface material modification that is economically and environmentally friendly. This method can be applied in ambient pressure that makes this method more feasible. The discharge of plasma from the plasma jet can be adjusted according to the design used. Carrier gas that is used in the plasma jet system can also be adapted to the needs or appropriate to the target material. The gases that can be used are helium, argon, etc. A variant gas flow rate will also affect the plasma species and the surface material characteristics produced. Modifying a material with certain compounds can be done by passing the active gases or vapors through the carrier gas. The use of the plasma jet method possibly converts the surface material to be hydrophobic or hydrophilic characteristics. Moreover, the plasma jet technique is applicable for various materials or substrates in any dimension. This review article will discuss the parameters applied, such as various designs, carrier gas, gas flow rates, power used in the plasma jet.
Development of high purity amorphous silica from emulsifier silicon by pyrolysis process at temperature of 700 oC
Authors: Prasetyo A B , Handayani M , Sulistiyono E , Syahid A N , Febriana E , Mayangsari W , Muslih E Y , Nugroho F , Firdiyono F
Published: March 2022

Silica in amorphous form is one of the fillers that is indispensable for the industrial world, especially for the superior material industry. Amorphous silica in the form of cristobalite compounds are inert, soft, and have high porosity which is suitable to be used as certain filler materials. This research describes about the characterization of amorphous silica produced from the pyrolysis process of emulsifier silicon. The pyrolysis process was carried out in three-stages, starting from the separation of water, separation of the emulsifier material from silica compound at a temperature of 300oC followed by pyrolysis at a temperature of 700 oC. In this process, amorphous silica and carbon are formed at the end of the pyrolysis process. In this study, characterization was carried out using XRD to determine the phase of the composition of the compound, SEM EDX to determine the morphology, and XRF analysis to determine the purity of product composition. The results of the XRD shows that the amorphous silica formed. SEM-EDX analysis shows that the amorphous silica has spherical fine grain with average particle size 0.30006 ± 0.01722 |am. It was supported by XRF analysis that shows that the amorphous silica has SiO2 content 99,92%.
Optimization of edible film based on chitosan-L-lysine incorporating cinnamon essential oil using response surface methodology
Authors: Utami M R , Kusumaningsih T , Firdaus M , Istiqomah A
Published: March 2022

An effective antibacterial edible film made from chitosan-l-lysine incorporating cinnamon essential oil were developed. This study aims to optimize the effectiveness of chitosan, L-lysine, and Cinnamon essential oil concentration to against some foodborne pathogens using a Box-Behnken designs (BBDs) with Response Surface Methodology (RSM). Based on the statistical analysis, L-lysine and cinnamon essential oil has the significance effect to against the foodborne pathogens (Staphylococcus epidermidis, Staphylococcus aureus, Escherichia coli and Salmonella enteritidis) proved by the p value<0.5 and the increase of bacteria in inhibition zone. The result showed the optimum formulation of edible film is chitosan 0.71g, L-lysine 0.5g, and Cinnamon essential oil 0.75ml.
Reinforcement to concrete bond strength: a comparison between normal concrete and various types of concrete
Authors: Rohman R K , Kristiawan S A , Saifullah H A , Basuki A
Published: March 2022

This paper describes the bond strength comparison between concrete and reinforcement with several types of concrete. The types of concrete studied were normal concrete (NC), Self-Compacting Concrete (SCC), High-Volume Fly Ash Concrete (HVFAC), and High-Volume Fly Ash Self-Compacting Concrete (HVFA-SCC). Research data were obtained from previous studies. The data of concrete bond strength were obtained by testing the reinforced concrete beam with a lap splice in the tensile moment area. Bond strength values were normalized by dividing with the square root of concrete grade. Then use normalized data to formulate the relationship between the length of lap splice to diameter ratio (ls/db) and the normalized bond strength concrete for both normal concrete and SCC. From the obtained relationship, we can compare the bond strength between NC and SCC. The SCC bond strength is higher than NC. Bond strength of HFVAC and HVFA-SCC is also higher than NC and SCC, so that the use of HVFA-SCC can reduce the need for lap splice.
The Impact of Electronic Procurement on the Maintenance and Rehabilitation System of the Surakarta Health Polytechnic Building
Authors: Santoso S B , Sangadji S , Suprapto M , Setyawan A
Published: March 2022

This study aims to determine the implementation of the procurement and maintenance system of buildings at the Surakarta Health Polytechnic, the obstacles that occur in the implementation of the procurement and maintenance system of buildings at the Surakarta Health Polytechnic. This research is a qualitative research with a phenomenological approach. The technique of taking research subjects used was purposive sampling. Sources of data used are sources, events or activities, locations and documents and archives. The power gathering techniques used are interviews, archives and documentation. The validity of the data using interactive model analysis, namely data reduction, data presentation and conclusions.The results of this study indicate that the activities of implementing procurement and building maintenance services at the Surakarta Health Polytechnic include: planning, work programs, third party coordination, checking and selecting partners, so that the procurement and maintenance system of buildings runs well. Efforts made are financial proposals submitted in advance of the previous year, independent finance for each department used for minor maintenance, as well as an inventory of damage to each building with selection in building and building maintenance on the proposed priority scale.
Effect of the combination of Alpha-Cellulose and Polyvinyl Alcohol on physicochemical properties of Moringa oleifera leaves ethanolic extract patch and release test
Authors: Ermawati D E , Fitriani E R , Rohmani S , Kundarto W
Published: March 2022

Moringa oleifera oleifera Lam leave contains quercetin which has anti-inflammatory activity, with the mechanism of action reducing mast cell activity through the NF-kB pathway. The topical patch of Moringa oleifera leave ethanolic extract was develop as an alternative to oral anti-inflammatory side effects, including first-pass metabolism and gastric irritation. Polymer is the main component of a patch matrix system because it functions to control drug release. Alpha-cellulose (AC) and polyvinyl alcohol (PVA) are hydrophilic polymers with different properties and functions. PVA forms a pore that can control the drug release while AC has a strong barrier film so that the polymer combination can produce a patch matrix that meets the requirements. The combination of PVA and AC with a ratio of 1:2; 1:1; 2:1; then analyze for organoleptic, thickness, weight, folding endurance, moisture content, and pH. The concentration of quercetin in extracts and patch, and in vitro test. Statistical analysis was carried out to determine the effect of polymer combination. The results showed the combination of PVA and AC patch matrix of Moringa oleifera leaves extract had a significant effect on the physicochemical properties there are thickness, patch weight, and moisture content, but they did not affect folding endurance and pH. The ratio of PVA and AC of 1:2 is the chosen formula because it meets the patch requirements. The concentrations of quercetin in the extract is 14.21% w/w. The percentage of total flavonoid that released from patch was 37.23% for 5 hours. The release kinetics followed the Higuchi kinetics model with a diffusion mechanism.
Synthesize of Cerium-doped ZnO nanoparticles as antioxidant agent
Authors: Asma F , Prasetyo W , Priyono  , Nurhasanah I
Published: March 2022

Zinc oxide nanoparticles are potential metal oxide for antioxidant agent. This paper investigates antioxidant activity of cerium-doped zinc oxide (Ce-doped ZnO) nanoparticles. Ce-doped ZnO nanoparticles was prepared by precipitation method with calcination temperature of 200˚C. The product of precipitate was characterized by X-ray diffraction measurement, and UV-Vis spectrophotometer. The antioxidant activity of Ce-doped ZnO nanoparticles was investigated using 1,1-diphenyl-2-pcrylhydrazyl (DPPH) method. The X-ray diffraction pattern showed the growth of Ce-doped ZnO crystalline structure of hexagonal wurtzite with crystallite size of 42 nm. UV-Vis absorbance spectrum analysis revealed the band gap energy of Ce-doped ZnO nanoparticles was smaller than band gap energy of bulk ZnO. Ce-doped ZnO nanoparticles could scavenge DPPH free radicals and exhibited moderate antioxidant activity.
Monitoring and Energy Analysis of Plasma Discharge in Ozone Generator
Authors: Yusuf M M , Anwar M , Septian I R , Ibrahim M H , Saraswati T E
Published: March 2022

Ozone can be produced by plasma processing. Plasma is the fourth form of matter after gas when the gas is energized to be ionized or charged. To achieve efficient energy, the monitoring plasma production process is required. In this study, the plasma analysis was successfully carried out using simultaneous current-voltage measurement. The equipment was set in an ozone plasma generator consisting of an MQ-131 gas ozone sensor, PZEM-004T power sensor, DHT22 sensor for room temperature and humidity, MLX-90614 infrared temperature sensor, and Arduino Mega 2560, connected to an oscilloscope. Ozone device and sensors give and extract data to measure power and the ionization energy in ozone generation. The calculation results show the ionization energy with the highest value of 8.4 x 10“7 loule and the lowest value of 2.82xl014Ioule.
Resampling schemes in population annealing — numerical results
Authors: Gessert Denis , Weigel Martin , Janke Wolfhard
Published: March 2022

Population annealing (PA) is a population-based algorithm that is designed for equilibrium simulations of thermodynamic systems with a rough free energy landscape. It is known to be more efficient in doing so than standard Markov chain Monte Carlo alone. The algorithm has a number of parameters that can be fine-tuned to improve performance. While there is some theoretical and numerical work regarding most of these parameters, there appears to be a gap in the literature concerning the role of resampling in PA. Here, we present a numerical comparison of a number of resampling schemes for PA simulations of the 2D Ising model.
Phase diagram of the dodecahedron spin model on square lattice with diluted bonds
Authors: Yunita S. , Rahmat R. , Surungan T.
Published: March 2022

We study the effect of bond dilution of a dodecahedron spin model on ferromagnetic square lattice. The dodecahedron spin constitutes a discrete (polyhedral) counterpart of the continuous Heisenberg spin. Previous work found that, in the absence of dilution, the ferromagnetic dodecahedron system exhibits a finite temperature phase transition. We use Monte Carlo simulation with Wolff cluster algorithm to monitor how phase transitions are impacted by the bond dilution. We simulate the model with various bond concentrations and investigate the resulting phase diagram and critical behavior.
A simple method to accelerate configurational sampling for a generalized hybrid Monte Carlo method
Authors: Suzuki D , Hori T , Miura S
Published: March 2022

In this paper, a simple method to improve sampling efficiency of the generalized hybrid Monte Carlo (GHMC) method is presented. Compared to the standard GHMC method, our method is found to allow us to safely increase the time increment for solving an equation-of-motion in the GHMC calculations by a factor of 4. We have demonstrated various algorithmic parameter dependence on the sampling efficiency of a hydrated alanine dipeptide.
Interaction between PET tracer and the specific residues around the gate of the open form of Monoamine Oxidase B (MAO-B)
Authors: Ottawa M , Miyashita N
Published: March 2022

Monoamine Oxidase B (MAO-B) is the enzyme that metabolizes a monoamine neurotransmitter. Recently, a PET tracer targeting MAO-B, SMBT-1, has been developed as the biomarker of neurodegenerative diseases. However, the detailed binding mode of SMBT-1 has not been clear. To clarify the binding mode of SMBT-1 on MAO-B, we performed the molecular dynamics (MD) simulations of MAO-B in the outer mitochondrial membrane and the complex of MAO-B to SMBT-1, and the docking simulation of MAO-B with SMBT-1. We found that the Leu88, Leu171, Ile199, and Tyr326around the substrate-binding site interact with SMBT-1. These hydrophobic residues mainly support the two aromatic rings of the center of SMBT-1, making the stable binding of SMBT-1.
Role of temperature and alignment activity on kinetics of coil-globule transition of a flexible polymer
Authors: Paul Subhajit , Majumder Suman , Janke Wolfhard
Published: March 2022

We study the nonequilibrium kinetics during the coil-globule transition of a flexible polymer chain with active beads after a quench from good to poor solvent condition using molecular dynamics simulation. Activity for each bead is introduced via the well-known Vicsek-like alignment rule due to which the velocity of a bead tries to align towards the average direction of its neighbors. We investigate the role of quenching temperature with varying activity during collapse of this polymer. We find that although for lower activities the kinetics remains qualitatively similar for different temperatures, for higher activity noticeable differences can be identified.
Compressed sensing based on QUBO formulation
Authors: Kudo Kazue
Published: March 2022

Ising machines efficiently solve the combinatorial optimization problems described by the Ising model or the quadratic unconstrained binary optimization (QUBO) formulation. A hybrid method based on the QUBO formulation for compressed sensing is proposed. The proposed method comprises alternative steps of discrete and continuous optimization. In the discrete optimization step, the objective function is described by the QUBO formulation. Successful examples obtained via the proposed method are demonstrated. The performance of the proposed method depends highly on the initial conditions.
The formation of dark-matter-deficient galaxies through galaxy collisions
Authors: Otaki Koki , Mori Masao
Published: March 2022

In the standard galaxy formation model, cold dark matter (CDM) drives the hierarchical structure formation. However, recently it is suggested that the satellite galaxy NGC1052-DF2, a member of the elliptical galaxy NGC1052 group, has a very little dark matter component compared to the theoretical predictions. 27 dark-matter-deficient galaxies have been discovered, but it is difficult to explain their formation process in the CDM model. We investigate the formation process through dark matter subhalo (DMSH) collisions using three-dimensional numerical simulations. As a result, we show the bifurcation sequence of the formation of dark-matter-dominated galaxies and dark-matter-deficient galaxies. In the case of low-speed collisions, a merger of the two DMSHs produces dark-matter-dominated galaxies. However, the two DMSHs penetrate each other, but the gaseous mediums collide for the middle-speed encounter. The enhancement of the gas density induces a burst of star formation, and then a dwarf galaxy without a dark matter halo forms at the interface of the DMSH collision.
Transformations of fast neutron-irradiated diamonds under femtosecond laser radiation
Authors: Khomich A A , Kononenko V V
Published: March 2022

Graphitization of the (111) face of diamond irradiated with fast neutrons under single pulses of the third harmonic of a Ti: sapphire laser (100 fs, 266 nm) is investigated. Transformations of the structure of the graphitized material along the surface of laser spots formed by the pulses at different energies are investigated by confocal Raman spectroscopy. It is found that irradiation of diamond with fast neutrons lowers the graphitization threshold by about five times compared with that of unirradiated diamond.
Hydrothermal zinc oxide nanostructures: geometry control and narrow band UV emission
Authors: Kadinskaya S A , Kondratev V M , Kindyushov I K , Labzovskaya M E , Novikov B V , Shtrom I V , Lihachev A I , Nashchekin A V , Bolshakov A D
Published: March 2022

In this work we study zinc oxide nanostructures of various geometries synthesized via the hydrothermal technique on Si (111) substrate. We demonstrate capabilities of the growth protocol for control over the morphology of nanostructures varying from nanowires to hexapods. The obtained samples were studied by photoluminescence spectroscopy to demonstrate a very narrow spontaneous emission near 370 nm. Despite cheap and feasible fabrication, the obtained nanostructures possess high crystallinity confirmed by the absence of typical for ZnO wide emission band in the visible region, related with the structure imperfections. This property together with the capabilities of the geometrical control over the nanostructures unveil perspectives of the reported approach for future UV photonic applications.
Investigation of infrared photoluminescence spectra of Ge1-x-y
Si
x
Sn
y
/Si nanostructures
Authors: Kolyada D V , Karaborchev A A , Firsov D D , Mashanov V I , Timofeev V A , Komkov O S
Published: March 2022

This work investigates the luminescence properties of pseudomorphic nanostructures with Ge1-x-y
Si
x
Sn
y
/Si superlattices (SL) grown on silicon substrates by molecular beam epitaxy. It was shown that the addition of Sn (y = 0.07) to the alloy layers within the structures results in a significant shift of the photoluminescence (PL) spectra towards longer wavelengths (2.0-3.5 μm) compared to similar Ge0.7Si0.3/Si superlattices. A series of experiments involving etching the structures to different depths have shown that the observed photoluminescence occurs exactly in the Ge1-x-y
Si
x
Sn
y
/Si SL region, with the sublinear nature of the PL power dependence indicating the probable participation of defects in radiative recombination. A significant increase in low-temperature PL was observed with a decrease in the thickness of narrow-gap SL layers from 6 to 2 nm, as well as with an increase in the number of superlattice periods from 10 to 30. The obtained structures exhibit relatively good temperature stability of luminescence, which is preserved up to 160 K. Thus, the current work demonstrates the possibility of creating mid-wave IR emitting epitaxial structures on silicon substrates.
Exciton-polariton dispersion in an A
III
B
V
total internal reflection planar waveguide with a quantum well
Authors: Mitryakhin V N , Shapochkin P Yu , Lozhkin M S , Efimov Yu P , Eliseev S A , Kapitonov Yu V
Published: March 2022

In this work we propose means to determine the dispersion of light in a semiconductor total internal reflection (TIR) planar waveguide featuring dielectric response of excitons from a quantum well (QW). The given theoretical apparatus is then used to reproduce the data experimentally acquired when probing the AlGaAs-based waveguide (with a GaAs QW in its waveguiding layer) with a continuous laser through a coupling grating and then gathering the light transmitted through the waveguiding layer.
Photoluminescence study of InP and In(As, P) inclusions into Si (100) substrate
Authors: Melnichenko I A , Dragunova A , Kryzhanovskaya N V , Viazmitinov D V , Semenova E , Berdnikov Y
Published: March 2022

We present a photoluminescence study of In(As,P) monolithic nanoinclusions into Si (100) substrates. The structures were grown in openings of the silicon substrates using an original approach based on the metal-organic vapor epitaxy method. The obtained arrays of In(As,P) nanoinclusions into the Si (100) surface were investigated by scanning microphotoluminescence spectroscopy. The obtained results show high crystalline quality of In(As,P) inclusions with broad emission peak in the near-infrared range of wavelengths.
Control of the morphology of silver dendrites formed by glass electrolysis
Authors: Lubyankina E A , Babich E S , Lipovskii A A , Kryzhanovskaya N V
Published: March 2022

We demonstrate a new technique to fabricate silver dendritic structures in a subsurface glass layer based on electrolysis of silver-enriched glass. Chemical etching of glass in water diluted HF allows “opening” of the dendrites for their characterization, which makes possible their use for Surface-enhanced Raman scattering. The structure and morphology of the dendrites were characterized using atomic force and scanning electron microscopy, and energy-dispersive X-ray spectroscopy. It was demonstrated that the surface morphology of the formed structures depends on the electric charge passed through the sample during the electrolysis and the duration of the chemical etching. The presented method does not require expensive equipment and materials and allows one to form silver nanostructures of a prescribed pattern.
Module development for the ATLAS ITk pixel detector
Authors: Möbius S.
Published: March 2022

After the upgrade of the LHC to the high-luminosity-LHC, the instantaneous luminosity will reach unprecedented values, resulting in about 200 proton-proton interactions in a typical bunch crossing. The current ATLAS inner detector will be replaced by an all-silicon system, the Inner Tracker. The innermost part of the Inner Tracker will consist of a state-of-the-art pixel detector. The individual modules of the Inner Tracker pixel detector comprise silicon sensors using various different technologies, with the sensors readout using the new ITkPix ASIC.
Automated visual inspection and defect detection of large-scale silicon strip sensors
Authors: Affolder K. , Ciocio A. , Cornell E. , Fadeyev V. , Luce Z. , Gunnell J. , Martinez-McKinney F. , Johnson T. , MacFadyen R. , Poley L. , Wilson K.
Published: March 2022

For the Phase-II Upgrade of the ATLAS Detector, the Inner
Detector will be replaced with the Inner Tracker (ITk), consisting
of a pixel and a strip tracker. The 17,888 silicon strip detector
modules comprising the ITk strip tracker will be assembled from
silicon strip sensors and flexes with readout chips in a manual
assembly process performed at 20 module assembly sites in a complex
distribution chain, which requires quality control steps to be
performed after each distribution and assembly step.

Sensor quality control requires a visual inspection of the full
sensor area (about 100 cm2) of each sensor to detect and log any
defects (e.g. scratches, breakdown areas or chipped corners) or
contamination. Since manual surveys of full sensor areas for several
thousand sensors are both time-consuming and prone to errors,
alternative methods were investigated to automate the process and
improve its reliability.

This paper presents a setup developed to take high-resolution images
of full silicon strip sensors with high repeatability quickly and an
algorithm developed for the automated detection of defects, built
using functions and filters from popular open-source visual
processing packages OpenCV and Scikit-image. Methods were developed
both for small-scale high-resolution images and full-size sensor
images with lower resolution — both are presented here.
Gamma matrices, Majorana fermions, and discrete symmetries in Minkowski and Euclidean signature
Authors: Stone Michael
Published: March 2022

I describe the interplay between Minkowski and Euclidean signature gamma matrices, Majorana fermions, and discrete and continuous symmetries in all spacetime dimensions. In particular I argue that the space-time dimensions in which various classes of Majorana fermions exists are the same in both Minkowski and Euclidean signature.
Exact percolation probabilities for a square lattice: site percolation on a plane, cylinder, and torus
Authors: Akhunzhanov R K , Eserkepov A V , Tarasevich Y Y
Published: March 2022

We have found analytical expressions (polynomials) of the percolation probability for site percolation on a square lattice of size L × L sites when considering a plane (the crossing probability in a given direction), a cylinder (spanning probability), and a torus (wrapping probability along one direction). Since some polynomials are extremely cumbersome, they are presented as separate files in supplemental material. The system sizes for which this was feasible varied up to L = 17 for a plane, up to L = 16 for a cylinder, and up to L = 12 for a torus. To obtain a percolation probability polynomial, all possible combinations of occupied and empty sites have to be taken into account. However, using dynamic programming along with some ideas related to the topology, we offer an algorithm which allows a significant reduction in the number of configurations requiring consideration. A rigorous formal description of the algorithm is presented. Divisibility properties of the polynomials have been rigorously proved. Reliability of the polynomials obtained have been confirmed by the divisibility tests. The wrapping probability polynomials on a torus provide a better estimate of the percolation threshold than that from the spanning probability polynomials. Surprisingly, even a naive finite size scaling analysis allows an estimate to be obtained of the percolation threshold p

c
= 0.592 69.
The Judgment of the Appeals Chamber of the International Criminal Court of 5 March 2020 in the Case of Afghanistan
Authors: Bula-Bula Sayeman
Published: March 2022

This study seeks to show that the Appeals Chamber of the ICC responsible for the ruling on the case of the armed conflict in Afghanistan has made an inchoate historic judgment. The analysis focuses on two main points: First, the reasoning made by the Prosecutor that the Pre-Trial Chamber abused its discretion in assessing the “interests of justice”; and second, the assessment of the scope of the procedural act. Finally, the unprecedented ruling of the ICC can consolidate the progressive positivism which now seems to be spreading across many areas of international law.
Self-assembly synthesis of diorganotin complexes based on arylformylhydrazone possessing ONO donor set: anticancer activity and mechanism
Authors: Jiang Wujiu , Zhang Zhijian , Ni Penghui , Tan Yuxing
Published: March 2022

Fourteen new organotin(IV) complexes were successfully synthesized and characterized by elemental analyses, Fourier transform infrared spectroscopy (FT-IR), multinuclear (1H, 13C, and 119Sn) NMR spectroscopy, high-resolution mass spectrometry (HRMS), and X-ray single-crystal techniques. Crystallographic data showed that the complexes 1b, 2b, 3b, and 5b were macrocyclic compounds, 4b exhibited a one-dimensional spiral chain structure with distorted trigonal bipyramidal geometry, other complexes were centrosymmetric dimers, and there was an Sn2O2 four-membered ring in the middle of the molecule. In-vitro anticancer activity against the three human tumor cell lines NCI-H460, MCF-7, and HepG2 was studied, and the dibutyltin complex 5a is a more potent antitumor agent than other complexes and cisplatin. Cell apoptosis study of 5a with the highest activity on HepG2 cancer cell lines was done by flow cytometry; it was shown that the antitumor activity of 5a was related to apoptosis, and it inhibited proliferation by blocking cells in the G2/M phase. The single-cell gel electrophoresis assay results show that 5a induces DNA damage. 5a interacts with ct-DNA by intercalating the mode of interaction. UV–visible absorption spectrometry, fluorescence competitive, viscosity measurements, and gel electrophoresis results also support the intercalative mode of interaction for 5a with DNA.
APYRASE1/2 mediate red light-induced de-etiolation growth in Arabidopsis seedlings
Authors: Weeraratne Gayani , Wang Huan , Weeraratne Tharindu P , Sabharwal Tanya , Jiang Han-Wei , Cantero Araceli , Clark Greg , Roux Stanley J
Published: March 2022

In etiolated seedlings, red light (R) activates phytochrome and initiates signals that generate major changes at molecular and physiological levels. These changes include inhibition of hypocotyl growth and promotion of the growth of primary roots, apical hooks, and cotyledons. An earlier report showed that the sharp decrease in hypocotyl growth rapidly induced by R was accompanied by an equally rapid decrease in the transcript and protein levels of two closely related apyrases (APYs; nucleoside triphosphate-diphosphohydrolases) in Arabidopsis (Arabidopsis thaliana), APY1 and APY2, enzymes whose expression alters auxin transport and growth in seedlings. Here, we report that single knockouts of either APY inhibit R-induced promotion of the growth of primary roots, apical hooks, and cotyledons, and RNAi-induced suppression of APY1 expression in the background of apy2 inhibits R-induced apical hook opening. When R-irradiated primary roots and apical hook-cotyledons began to show a gradual increase in their growth relative to dark controls, they concurrently showed increased levels of APY protein, but in hook-cotyledon tissue, this occurred without parallel increases in their transcripts. In wild-type seedlings whose root growth is suppressed by the photosynthesis inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea, the R-induced increased APY expression in roots was also inhibited. In unirradiated plants, the constitutive expression of APY2 promoted both hook opening and changes in the transcript abundance of Small Auxin Upregulated RNA (SAUR), SAUR17 and SAUR50 that help mediate de-etiolation. These results provide evidence that the expression of APY1/APY2 is regulated by R and that APY1/APY2 participate in the signaling pathway by which phytochrome induces differential growth changes in different tissues of etiolated seedlings.
The moving crude adiabatic alternative to the adiabatic representation in excited state dynamics
Authors: Maskri Rosa , Joubert-Doriol Loïc
Published: March 2022

The choice of the electronic representation in on-the-fly quantum dynamics is crucial. The adiabatic representation is appealing since adiabatic states are readily available from quantum chemistry packages. The nuclear wavepackets are then expanded in a basis of Gaussian functions, which follow trajectories to explore the potential energy surfaces and approximate the potential using a local expansion of the adiabatic quantities. Nevertheless, the adiabatic representation is plagued with severe limitations when conical intersections are involved: the diagonal Born–Oppenheimer corrections (DBOCs) are non-integrable, and the geometric phase effect on the nuclear wavepackets cannot be accounted for unless a model is available. To circumvent these difficulties, the moving crude adiabatic (MCA) representation was proposed and successfully tested in low energy dynamics where the wavepacket skirts the conical intersection. We assess the MCA representation in the case of non-adiabatic transitions through conical intersections. First, we show that using a Gaussian basis in the adiabatic representation indeed exhibits the aforementioned difficulties with a special emphasis on the possibility to regularize the DBOC terms. Then, we show that MCA is indeed able to properly model non-adiabatic transitions. Tests are done on linear vibronic coupling models for the bis(methylene) adamantyl cation and the butatriene cation.

This article is part of the theme issue ‘Chemistry without the Born–Oppenheimer approximation’.
Rv0233 is not essential for the survival of Mycobacterium tuberculosis in stress conditions
Authors: Ikeh Melanie A. , Parish Tanya
Published: March 2022

Mycobacterium tuberculosis is an important global pathogen. We were interested in understanding the role of Rv0233, a proposed subunit of the class IB ribonucleotide reductase. We constructed an in-frame, unmarked deletion strain of M. tuberculosis and characterized its growth and survival under replicating and non-replicating conditions. We confirmed previous studies that Rv0233 is not essential for aerobic growth or survival in the presence of nitrite. We demonstrate that the deletion of Rv0233 does not affect susceptibility to frontline tuberculosis drugs or hydrogen peroxide. The deletion strain survived equally well under nutrient starvation or in hypoxia and was not attenuated for growth in macrophages.
Optimized production and fluorescent labelling of SARS-CoV-2 Virus-Like-Particles to study virus assembly and entry
Authors: Gourdelier Manon , Swain Jitendriya , Arone Coline , Mouttou Anita , Bracquemond David , Merida Peggy , Saffarian Saveez , Lyonnais Sébastien , Favard Cyril , Muriaux Delphine
Published: March 2022

SARS-CoV-2 is an RNA enveloped virus responsible for the COVID-19 pandemia that conducted in 6 million deaths worldwide so far. SARS-CoV-2 particles are mainly composed of the 4 main structural proteins M, N, E and S to form 100nm diameter viral particles. Based on productive assays, we propose an optimal transfected plasmid ratio mimicking the virus RNA ratio allowing SARS-CoV-2 Virus-Like Particle (VLPs) formation composed of the viral structural proteins M, N, E and S. Furthermore, monochrome, dual-color fluorescent or photoconvertible VLPs were produced. Thanks to live fluorescence and super-resolution microscopy, we quantified VLPs size and concentration. It shows a diameter of 110 and 140 nm respectively for MNE-VLPs and MNES-VLPs with a minimum concentration of 10e12 VLP/ml. SARS-CoV-2 VLPs could tolerate the integration of fluorescent N and M tagged proteins without impairing particle assembly. In this condition, we were able to establish incorporation of the mature Spike in fluorescent VLPs. The Spike functionality was then shown by monitoring fluorescent MNES-VLPs docking and endocytosis in human pulmonary cells expressing the receptor hACE2. This work provides new insights on the use of non-fluorescent and fluorescent VLPs to study and visualize the SARS-CoV-2 viral life cycle in a safe environment (BSL-2 instead of BSL-3). Moreover, optimized SARS-CoV-2 VLP production can be further adapted to vaccine design strategies.
Blood-derived DNA methylation clusters associate with adverse social exposures and endophenotypes of stress-related psychiatric illness in a trauma-exposed cohort of women
Authors: Pfeiffer JR , van Rooij Sanne J.H. , Mekawi Yara , Fani Negar , Jovanovic Tanja , Michopoulos Vasiliki , Smith Alicia K. , Stevens Jennifer S. , Uddin Monica
Published: March 2022

Adverse social exposures (ASEs) such as low income, low educational attainment, and childhood/adult trauma exposure are associated with variability in brain region measurements of grey matter volume (GMV), surface area (SA), and cortical thickness (CT). These CNS morphometries are associated with stress-related psychiatric illnesses and represent endophenotypes of stress-related psychiatric illness development. Epigenetic mechanisms, such as 5-methyl-cytosine (5mC), may contribute to the biological embedding of the environment but are understudied and not well understood. How 5mC relates to CNS endophenotypes of psychiatric illness is also unclear.

In 97 female, African American, trauma-exposed participants from the Grady Trauma Project, we examined the associations of childhood trauma burden (CTQ), adult trauma burden, low income and low education with blood-derived 5mC clusters and variability in brain region measurements in the amygdala, hippocampus and frontal cortex subregions. To elucidate whether peripheral 5mC indexes CNS endophenotypes of psychiatric illness, we tested whether 73 brain/blood correlated 5mC clusters, defined by networks of correlated 5mC probes measured on Illumina’s HumanMethylation Epic Beadchip, mediated the relationship between ASEs and brain measurements.

CTQ was negatively associated with rostral middle frontal gyrus (RMFG) SA (β = - 0.231, p = 0.041). Low income and low education were also associated with SA or CT in a number of brain regions. Seven 5mC clusters were associated with CTQ (pmin = 0.002), two with low education (pmin = 0.010), and three with low income (pmin = 0.007). Two clusters fully mediated the relation between CTQ and RMFG SA, accounting for 47% and 35% of variability respectively. These clusters were enriched for probes falling in DNA regulatory regions, as well as signal transduction and immune signaling gene ontology functions. Methylome-network analyses showed enrichment of macrophage migration (p = 9×10-8), T cell receptor complex (p = 6×10-6), and chemokine-mediated signaling (p = 7×10-4) pathway enrichment in association with CTQ.

Our results support prior work highlighting brain region variability associated with ASEs, while informing a peripheral inflammation-based epigenetic mechanism of biological embedding of such exposures. These findings could also serve to potentiate increased investigation of understudied populations at elevated risk for stress-related psychiatric illness development.
DNA Methylation Dynamics and Dysregulation Delineated by High-Throughput Profiling in the Mouse
Authors: Zhou Wanding , Hinoue Toshinori , Barnes Bret , Mitchell Owen , Iqbal Waleed , Lee Sol Moe , Foy Kelly K. , Lee Kwang-Ho , Moyer Ethan J. , VanderArk Alexandra , Koeman Julie M. , Ding Wubin , Kalkat Manpreet , Spix Nathan J. , Eagleson Bryn , Pospisilik John Andrew , Szabó Piroska E. , Bartolomei Marisa S. , Vander Schaaf Nicole A. , Kang Liang , Wiseman Ashley K. , Jones Peter A. , Krawczyk Connie M. , Adams Marie , Porecha Rishi , Chen Brian H. , Shen Hui , Laird Peter W.
Published: March 2022

We have developed a mouse Infinium DNA methylation array that contains 297,415 probes to capture the diversity of mouse DNA methylation biology. We present a mouse DNA methylation atlas as a rich reference resource of 1,239 DNA samples encompassing distinct tissues, strains, age, sex, and pathologies. We describe applications for comparative epigenomics, genomic imprinting, epigenetic inhibitors, PDX assessment, backcross tracing, and epigenetic clocks. We dissect DNA methylation processes associated with differentiation, aging and tumorigenesis. Notably, we find that tissue-specific methylation signatures localize to binding sites for transcription factors controlling the corresponding tissue development. Age-associated hypermethylation is enriched at regions of Polycomb repression, while hypomethylation is enhanced at regions bound by cohesin complex members. ApcMin/+ polyp-associated hypermethylation affects enhancers regulating intestinal differentiation, while hypomethylation targets AP-1 binding sites. This MM285 mouse array is widely accessible to the research community, and will accelerate future high sample-throughput studies in this important model organism.