bluuebunny/crossref_metadata_2025 huggingface dataset:
Nuclear wave-packet-propagation-based study of the electron-coupled, proton-transfer process in the charge-transfer state of FHCl exhibiting three electronic states in full-dimensional space
Authors: Ariyageadsakul Pinit , Baeck Kyoung Koo
Published: December 2022

The charge-transfer (CT) excited state of FHCl (F+H–Cl−), generated by the photodetachment of an electron from its precursor anion (FHCl−) by a photon energy of ∼9.5 eV, is a realistic prototype of two bidirectional-coupled reaction pathways, namely the proton-transfer (PT) and electron-transfer (ET) channels, that produce F + HCl and FH + Cl combinations, respectively. The early-time dynamics of the CT was studied via the time-dependent propagations of nuclear wave packets comprising three nonadiabatically coupled electronic states defined within a three-dimensional space. The detailed analyses of the early-time dynamics revealed an interesting phenomenon in which the onset of PT was ∼80 fs earlier than that of ET, indicating that PT dominated ET in this case. A more significant finding was that the proper adjustment of the electronic-charge distribution for the onset of ET was obtained ∼80 fs after the onset of PT; this adjustment was mediated by the initial movement of the H atom, i.e., the F–H vibration mode. To avail experimental observables, the branching ratio, χ = PT/(PT + ET), and absorption spectrum generating the neutral FHCl molecule from its precursor anion were also simulated. The results further demonstrated the dependences of the χs and spectrum on the change in the initial vibration level of the precursor anion, as well as the isotopic substitution of the connecting H atom with deuterium, tritium, and muonium.
Effect of cavitation evolution on power characteristics of tidal current turbine
Authors: Gao Yanjing , Liu Hongwei , Guo Guanzhu , Lin Yonggang , Gu Yajing , Ni Yiming
Published: December 2022

With the development of large-scale tidal current turbines and the increase in tidal current velocity, the possibility of cavitation increases. Furthermore, unsteady cavitation is a complicated multiphase flow that causes power degradation of tidal current turbine blade. There has been no comprehensive investigation of it so far. In this study, the blade captured power is obtained at different cavitation numbers using the Schnerr–Sauer cavitation model. The numerical uncertainty for the mesh and the time step is calculated by the grid convergence index method. It has been shown that, when the cavitation number is 5 and 2, cavitation has no effect on the blade power. With the decrease in the cavitation number, the rise in cavitation intensity occurs when the vapor distribution area stretches from the blade tip to the blade root and from the leading edge to the trailing edge, respectively. With a fall in cavitation number to 1.3, the vapor volume fraction rises, and the viscosity of the mixed phase reduces, resulting in a reduction in viscous power. When the cavitation number is 0.8, there exists a larger region in which an absolute value of minimum pressure coefficient is less than the cavitation number, a smaller blade load is present, and the pressure difference power is substantially decreased. Because of the huge inverse pressure gradient created by cavitation, the negative pressure difference power is generated, resulting in a decline of the blade power coefficient to 14%, when the cavitation number is 0.5.
Analytical Techniques for Hardness, Nanoindentation, and Elastic Modulus
Authors: K Namsheer , Rout Chandra Sekhar
Published: December 2022

The unique mechanical properties of 2D nanomaterials allow them for applications in many fields including tribology, nanofabrication, micromechanical devices, surface engineering, etc. Both computational and instrumental characterization techniques are widely followed to characterize the mechanical properties of 2D nanomaterials and properties including hardness, stress, strain, tensile strength and elastic modulus, etc. will play a crucial role in the performance of the synthesized nanomaterials. Instrumentation techniques like AFM, in situ AFM, pressurized blister test, etc. have been widely used to characterize the hardness, nanoindentation, and elastic modulus of 2D nanomaterials. The microscopic changes in physical/chemical properties of the nanomaterials will result in macroscopic changes in mechanical properties similarly, the atomic arrangements, crystallinity, molecular weight, and molecular mobility will drastically affect the mechanical properties. Here this chapter comprehensively discusses the different types of analytical techniques used for hardness, indentation, and elastic modulus of 2D materials.
Density Functional Theory: An Investigative and Predictive Tool for the Study of 2D Materials
Authors: Kadrekar Riddhi , Late Dattatray J.
Published: December 2022

Material characterization involves identification of material properties for synthesized material. Density Functional theory can evaluate material properties for diverse compositions, configurations, and morphology prior to material synthesis, thereby, gauging applicability of novel materials. This chapter includes an introductory and stepwise recipe for studying novel 2D materials using DFT, starting from establishing the synthesizability of a material, followed by understanding of its structural, electronic, optical, and mechanical properties and finally evaluating its applicability in varied application like catalysis, energy storage, energy production, sensing, super-capacitance, electronics, spintronics etc. Current chapter also includes charts that provide methodical guidelines to determine material applicability for popular applications.
Summary
Authors: Late Dattatray J. , Patra Abhinandan , Rout Chandra Sekhar
Published: December 2022

In this book, we have discussed the emergent 2D materials, which are going to be the frontiers in each and every aspect of the nanotechnology and optoelectronics world. However, the fruitful application of these 2D nanomaterials and the intrinsic and extrinsic properties have to be investigated thoroughly. Therefore, characterization techniques like optical based techniques, time resolved terahertz spectroscopy, Raman spectroscopy, x-ray based techniques, probe-based techniques, electron diffraction-based techniques, analytical techniques, etc., along with their theoretical attributes come in handy for exploring more and more about the novel 2D material. This book will also help to develop a protocol for the characterization of novel 2D materials for technological application. We have elaborated on all these characterization techniques with proper scientific discussions so as to establish a correlation with the properties and performance of newly discovered/synthesized 2D materials. All the primary principles involving these techniques, their instrumentation and the recent trends involving the characterization of 2D materials with the proposed techniques have been meticulously exemplified. However, there are some challenges that cannot be disregarded and must be looked into. The major critical challenges and future viewpoints of each of the techniques have been particularized in their respective chapters, yet a few overall comments have been included below.
Kin cannibals: recently hatched
Authors: Gould John , Mahony Stephen V. , Mahony Michael
Published: December 2022

Cannibalism is a behaviour exhibited across amphibian life history stages; however, there are few records that involve cannibalism between siblings. Here, we describe observations of recently hatched tadpoles of the frog Philoria pughi consuming sibling embryos with delayed or failed development. Our observations indicate that additional nutrition is obtained from the ingested embryos, despite tadpoles of species of Philoria being capable of endotrophic development. This discovery should be considered when establishing captive breeding colonies for Philoria species and needs further investigation in wild populations.
MipZ caps the plus-end of FtsZ polymers to promote their rapid disassembly
Authors: Corrales-Guerrero Laura , Steinchen Wieland , Ramm Beatrice , Mücksch Jonas , Rosum Julia , Refes Yacine , Heimerl Thomas , Bange Gert , Schwille Petra , Thanbichler Martin
Published: December 2022

The spatiotemporal regulation of cell division is a fundamental issue in cell biology. Bacteria have evolved a variety of different systems to achieve proper division site placement. In many cases, the underlying molecular mechanisms are still incompletely understood. In this study, we investigate the function of the cell division regulator MipZ from
Caulobacter crescentus
, a P-loop ATPase that inhibits the polymerization of the treadmilling tubulin homolog FtsZ near the cell poles, thereby limiting the assembly of the cytokinetic Z ring to the midcell region. We show that MipZ interacts with FtsZ in both its monomeric and polymeric forms and induces the disassembly of FtsZ polymers in a manner that is not dependent but enhanced by the FtsZ GTPase activity. Using a combination of biochemical and genetic approaches, we then map the MipZ–FtsZ interaction interface. Our results reveal that MipZ employs a patch of surface-exposed hydrophobic residues to interact with the C-terminal region of the FtsZ core domain. In doing so, it sequesters FtsZ monomers and caps the (+)-end of FtsZ polymers, thereby promoting their rapid disassembly. We further show that MipZ influences the conformational dynamics of interacting FtsZ molecules, which could potentially contribute to modulating their assembly kinetics. Together, our findings show that MipZ uses a combination of mechanisms to control FtsZ polymerization, which may be required to robustly regulate the spatiotemporal dynamics of Z ring assembly within the cell.
Signs of low energy availability in elite male volleyball athletes but no association with risk of bone stress injury and patellar tendinopathy
Authors: Sesbreno Erik , Blondin Denis P. , Dziedzic Christine , Sygo Jennifer , Haman François , Leclerc Suzanne , Brazeau Anne‐Sophie , Mountjoy Margo
Published: December 2022

Relative Energy Deficiency in Sport (RED‐S) syndrome is associated with undesirable health and performance outcomes. The aetiology of RED‐S syndrome is low energy availability (LEA). LEA has been reported in male athletes in various sports, but there is little information in team sports. Therefore, the aims of this study were to assess the point‐prevalence of surrogate markers of LEA in elite male volleyball players and examine the association between low and normal total‐testosterone (TES) on endocrine markers, resting metabolic rate, bone mineral density (BMD), and history of injury/illness. Using a cross‐sectional design, 22 elite male volleyball players underwent anthropometric, dual‐energy X‐ray absorptiometry (DEXA or DXA) and resting metabolic rate testing, bloodwork, dietary analysis, the three‐factor eating questionnaire–R18, injury/illness questionnaire and Victorian Institute of Sport Assessment – patellar tendon questionnaire. The primary finding of this investigation was that 36% of athletes had ≥2 surrogate markers of LEA. Although fasted insulin was lower and cortisol was higher in players with low‐total TES, low BMD, low RMR and various other endocrine markers linked to LEA were not observed. More research is required to define surrogate markers of LEA in male athletes.
Second-order dust perturbations of the non-flat FLRW model with the positive cosmological constant
Authors: Sikora Szymon
Published: December 2022

In this paper, a specific solution to the second-order cosmological perturbation theory is given. Perturbations are performed around any Friedmann–Lemaître–Robertson–Walker spacetime filled with dust and with a positive cosmological constant. In particular, with a possibly non-vanishing spatial curvature. The adopted symmetry condition allows us to simplify the equations, leaving us with a great deal of freedom to choose the density distribution. In the result, we get a relatively simple metric of an inhomogeneous cosmological model, which will give a perfect tool for studying the influence of the local inhomogeneities onto the cosmological observables.
Phosphor thermometry in heat transfer fluids and liquid organic hydrogen carrier systems using (Sr,Ca)SiAlN3:Eu2+
Authors: Bollmann Jonas , Hickl Franziska , Preuster Patrick , Zigan Lars , Wasserscheid Peter , Will Stefan
Published: December 2022

Temperature control in heat exchangers in reacting and non-reacting flows is of great importance for process optimization. In this context, phosphor thermometry is a promising technique for remote planar temperature sensing. The thermometry technique is based on exciting a luminescent material by a laser pulse and analyzing the subsequent phosphorescence signal. A particular interesting application is chemical hydrogen storage using liquid organic hydrogen carrier (LOHC) systems. The knowledge of temperature fields is of special interest for the characterization and understanding of hydrogen release from the carrier liquid. We investigated the luminescence properties of the thermographic phosphor (Sr,Ca)SiAIN3:Eu2+ (‘SCASN:Eu2+’) dispersed in different heat transfer fluids, in particular LOHC systems, using a newly developed calibration cell. As heat transfer fluids may be excited to fluorescence by the laser as well, their absorption and florescence behavior is studied to develop an excitation and detection concept for thermometry. We found strong absorption of the heat transfer fluids from the UV range to a wavelength of about 400 nm. In addition, fluorescence signals were found in the visible wavelength range, which can interfere with the phosphor emissions. These fluorescence signals should therefore be circumvented by utilizing the different luminescence decay times in the chosen detection strategy. For thermometry, the SCASN:Eu2+ particles were excited by a laser sheet of a 532 nm Nd:YAG laser. A spectrometer and photomultiplier tube (PMT) were used to detect the emission spectrum and phosphorescence decay time (PDT). Two temperature evaluation strategies were applied, which are based on either the intensity ratio of two spectral emission regions (two-color laser-induced phosphorescence) or the PDT. The results obtained show an applicable measurement range between 293 K and 598 K for the intensity ratio method with a maximum relative sensitivity of 0.12% K−1 at 293 K. For the PDT method, the phosphor allows measurements between 423 K and 598 K with a maximum relative sensitivity of 0.56% K−1 at 598 K.
A laser-induced dual ultrasonic wave method for noncontact load monitoring of pillar porcelain insulators
Authors: Zhao Zhou-Feng , Feng Qian , Hui Yang , Lu Kuang-Da , Li Xiao-Ying , Ye Bo , Zhang Jun , Song Tao
Published: December 2022

In this paper, a noncontact load monitoring method based on laser-induced synchronous ultrasonic surface wave and air wave is presented to improve the accuracy of load measurement on pillar porcelain insulator. In order to eliminate the measurement error caused by insulator deformation, a correction algorithm for surface wave velocity calculation is established by introducing the air wave propagation time. An experimental setup of the load measurement system for pillar porcelain insulators based on laser-induced dual ultrasonic waves was assembled. A load calibration experiment and load detection experiment were carried out under various bending and torsional loads. The results showed that the proposed method is effective to solve the problem of the surface wave propagation time changing abruptly, greatly increasing the accuracy of load measurement. In the monitoring experiments, the relative error between the calculated load value and the actual applied load value was small, the average measurement error of the bending load was 16.20%, and the average measurement error of the torsional load was 11.38%. This proved that the measurement of the insulator load value using a laser ultrasonic surface wave is more precise than the traditional methods, making it more suitable for engineering inspection.
Verifying the equation for centripetal force: an augmented reality approach
Authors: Vidak Andrej , Movre Šapić Iva , Mešić Vanes
Published: December 2022

Classroom experiments related to investigating the centripetal force are often underrepresented in the physics teaching practice. This is largely due to the fact that schools lack the proper equipment and teachers lack the time to perform the rather tedious data collection procedures which are characteristic for some of the traditional experimental setups. A possible solution to this problem is to develop and utilize alternative experimental setups within the digital environment. In fact, earlier research has shown that new generations of students are highly motivated to learn physics in digital environments and that these environments often provide at least as efficient learning of concepts as traditional environments. In this article, we present an augmented reality Android application named CEntripetalForceAR (CEFAR) that allows students to experimentally investigate how centripetal force depends on the period of orbital motion and the orbital radius. A possible pedagogical approach to using CEFAR is also described, including suggestions on how CEFAR can be used to overcome some of the most common misconceptions related to circular motion. A user experience survey which included 163 first-year university students showed that CEFAR can be awarded an excellent usability rating. Most students stated that the application helped them to improve their understanding about centripetal force either by visualization or by the possibility to explore cause and effect relationships.
Modeling mousetrap car motion with polynomial functions of time
Authors: Johnson Wes
Published: December 2022

Spring powered cars speed up and then slow down. This paper presents three different methods for modelling this motion. These models express the car’s position and velocity as polynomial functions of time. They can be constructed from only one distance and two time measurements. Mousetrap cars are ideal candidates to be modelled in this way because it is obvious when the spring stops acting to accelerate these cars. This paper presents a spreadsheet which generates positive vs. time and velocity vs. time graphs using these polynomial functions. Students can use this spreadsheet to learn more about the motion of their cars. This tool also enables students to view and evaluate several different representations of that motion.
The effect of pre-sintering and high-temperature infiltration on the properties of single-domain YBCO bulk superconductors by the Y + 011 top-seeded infiltration growth process
Authors: Abulaiti Abulizi , Yang Wan-Min , Wu Ting-Ting , Cui Yan-Lan
Published: December 2022

The top-seeded infiltration growth process (TSIG) is one of the most important methods for the fabrication of single-domain rare-earth barium copper oxide (REBCO) bulk superconductors. The performance of samples is in the main closely related to the quality of the solid phase pellets (SPPs). In this paper, we report a new method for optimizing the SPPs and properties of single-domain REBCO bulks, including sintering of the SPPs (Y2O3 + BaCuO2), infiltration of the Ba–Cu–O liquid phase and the melting growth process. A group of single-domain YBCO bulk superconductors with a diameter of 20 mm have been fabricated by the modified RE + 011 TSIG method. Both the levitation force and the trapped field of the samples increase at first and then decrease with increase in the sintering time. The largest levitation force of 42.8 N and trapped field of 0.41 T (77 K, 0.5 T) are obtained in the sample sintered at 1000 °C for 4.5 h; this is mainly related to the optimal microstructure of the pre-sintered SPPs and the YBCO bulk. These results indicate that pre-sintering and high-temperature infiltration is a very important method for controlling the microstructure and improving the physical properties of single-domain YBCO bulk superconductors.
Analysis and design of overmoded coaxial Ku-band Cerenkov high power microwave oscillator with high efficiency
Authors: Yang Chaochao , Meng Jin , Deng Bingfang , Wang Haitao
Published: December 2022

An overmoded coaxial Ku-band Cerenkov high power microwave oscillator with high efficiency is proposed. The distance between the inner and outer conductors of the slow wave structure (SWS) in the Cerenkov oscillator is smaller than the space wavelength of output microwave. The overmoded structure can increase the power capacity of the oscillator by increasing the transversal size of the device. The higher-order modes are introduced into the beam-wave interaction region intentionally, so that the intense relativistic electron beams (IREB) interacts with the fundamental and higher-order modes. Dual-mode operation leads impure mode component to output microwave, so the simple trapezoid inner conductor is designed to achieve mode purification and output pure TEM mode. The extractor is added at the end of the SWS, which enhances the axial electric field near the location and increases the modulation depth of the electron beam current passing through the region. The particle-in-cell (PIC) simulation results show that under the input power of 3.5 GW, the output microwave power is 1.8 GW, and the corresponding working efficiency is 51.4%, which is much higher than that of similar periodic devices. The mode of output microwave is pure TEM mode, and the maximum surface electric field intensity is 0.96 MV cm−1, which means that the probability of radio-frequency breakdown is low.
Relativistic thermodynamics on conveyor belt
Authors: Güémez J , Mier J A
Published: December 2022

Two thermodynamic processes are analysed by using a relativistic four-vector fundamental equation formalism: the launching of a projectile by forces produced by chemical reactions inside a cannon (equivalent to a person launching a ball) placed on a moving platform, a mechanical energy production process, and the Joule-Kelvin process implemented on a conveyor belt. Each process is first studied in frame S, in which the device—the cannon or the porous plug –, is at rest, obtaining its four-vector fundamental equation dE

μ
= δ
W

μ
+ δ
Q

μ
. Using the Lorentz transformation, the corresponding four-vector equation in frame

S

¯

—in which the processes are carried out on a moving platform or a conveyor belt—

d

E

¯

μ

=
δ

W

¯

μ

+
δ

Q

¯

μ

, is obtained, obeying Einstein’s principle of relativity. For the relativistic description to be coherent, one has to assign linear momentum to the non-mechanical energies and consider their variations in the corresponding Newton’s second law equation and the relativistic non-simultaneity and conveyor belt effects. In relativistic thermodynamics, Newton’s second law and the first law of thermodynamics are not independent equations. It is shown that entropy variations and fuel consumption are frame independent magnitudes.
Theoretical and computational study of a partially coherent laser beam in a marine environment
Authors: Chib Salma , Bayraktar Mert , Belafhal Abdelmajid
Published: December 2022

The propagation formula of a partially coherent Generalized Flattened Hermite-Cosh-Gaussian (GFHChG) beam in maritime atmospheric turbulence is derived with the help of the extended Huygens–Fresnel principle. In addition, the analytical expression for the beam width of a partially coherent GFHChG beam in the considered environment is investigated. From the numerical results based on the analytical formulae, we find that the analyzed beam can take different shapes of the profile, depending on the turbulence and beam parameters. And also, it can significantly resist turbulence with small wavelength and waist width values. On the other hand, when the medium becomes turbulent, the beam loses its characteristics and its resistance to fluctuations. Furthermore, the results reveal that the beam spreads more rapidly with the increase of the strength of turbulence, the outer scale size, and the decrease of the inner scale size. We should mention that the results gained represent a general form of numerous partially coherent laser beams such as Generalized Flattened Hermite Gaussian, Generalized Flattened Cosh-Gaussian, Hermite-Cosh-Gaussian, Cosh-Gaussian, Hermite-Gaussian and Gaussian Schell model beams.
Uncertainty relations for coherence quantifiers based on the Tsallis relative 1/2-entropies
Authors: Rastegin Alexey E
Published: December 2022

In quantum information science, systems with incomplete information are typically dealt with. To characterize quantumness from different viewpoints, several kinds of non-classical correlations should be described quantitatively. The concept of coherence within purely quantum framework is currently the subject of active research. A certain attention is paid to coherence quantifiers averaged with respect to a set of quantum ensembles or special measurements. Mutually unbiased bases and symmetric informationally complete measurements are important examples. We present uncertainty relations for quantum-coherence quantifiers based on the Tsallis relative 1/2-entropies. Together with mutually unbiased bases, the paper also deals with a measurement built of the states of an equiangular tight frame. The derived inequalities are exemplified with mutually unbiased bases and symmetric informationally complete measurement in two dimensions.
Energy property and covalency of H2S···X (X = N2, CO, CS and SiO) hydrogen bond
Authors: Xinying Li
Published: December 2022

CCSD(T) calculations on H2S…X (X = N2, CO, CS and SiO) series provide reliable structures, energy properties and covalency of hydrogen bonds (HB). Symmetry adapted perturbation theory analysis demonstrates the dominant role of electrostatic interactions for the relative stronger HBs; and the dispersion demonstrates the attraction of the very weak HB of H2S…N2. Upon formation of HBs, the electrostatic and dispersion energies play important role. The covalent character is analyzed by AIM theory and topological analysis on electron density functions; and it suggests the very weak strength of HBs with non-covalent character.
Enhanced topological superconductivity in an asymmetrical planar Josephson junction
Authors: Zhang Erhu , Zhang Yu
Published: December 2022

As a platform for holding Majorana zero models (MZMs), the two-dimensional planar topological Josephson junction that can be used as carriers for topological quantum computing faces some challenges. One is a combination of mirror and time-reversal symmetries may make the system hold multiple pairs of MZMs. The other is that a soft gap dominated by a large momentum occurs in a clean system. To solve these problems, asymmetric junction can be introduced. Breaking this symmetry changes the symmetry class from class BDI to class D, and only a single pair of MZMs can be left at the boundary of the system. We numerically study four cases that create an asymmetric system and find out different superconducting pairing potential, different coupling coefficients between two-dimensional electron gases (2DEGs) and two superconducting bulks, different widths of two superconducting bulks make the gap of the system decrease at the optimal value, but make the gap at the minimum value increases. And the zigzag-shape quasi-one-dimensional junction eliminates the large momentum parallel to the junction and enhances the gap at the large momentum. However, the zigzag-shape junction cannot increase the gap at the region of multiple pairs of MZMs in a symmetric system. We show that by combining zigzag-shape junction with different coupling coefficients, the system can maintain a large gap (≈0.2Δ) in a wide region of the parameter space.
Stress effect on lattice thermal conductivity of anode material NiNb2O6 for lithium-ion batteries
Authors: Chen Ao , Tong Hua , Wu Cheng-Wei , Xie Guofeng , Xie Zhong-Xiang , Xiang Chang-Qing , Zhou Wu-Xing
Published: December 2022

The thermal transport properties of NiNb2O6 as anode material for lithium-ion battery and the effect of strain were studied by machine learning interatomic potential combined with Boltzmann transport equation. The results show that the lattice thermal conductivity of NiNb2O6 along the three crystal directions [100], [010], and [001] are 0.947 W⋅m−1⋅K−1, 0.727 W⋅m−1⋅K−1, and 0.465 W⋅m−1⋅K−1, respectively, indicating the anisotropy of the lattice thermal conductivity of NiNb2O6. This anisotropy of the lattice thermal conductivity stems from the significant difference of phonon group velocities in different crystal directions of NiNb2O6. When the tensile strain is applied along the [001] crystal direction, the lattice thermal conductivity in all three directions decreases. However, when the compressive strain is applied, the lattice thermal conductivity in the [100] and [010] crystal directions is increased, while the lattice thermal conductivity in the [001] crystal direction is abnormally reduced due to the significant inhibition of compressive strain on the group velocity. These indicate that the anisotropy of thermal conductivity of NiNb2O6 can be enhanced by the compressive strain, and reduced by the tensile strain.
Power-law Distribution and Scale-invariant Structure from the First CHIME/FRB Fast Radio Burst Catalog
Authors: Wang Zi-Han , Sang Yu , Zhang Xue
Published: December 2022

We study the statistical property of fast radio bursts (FRBs) based on a selected sample of 190 one-off FRBs in the first CHIME/FRB catalog. Three power law models are used in the analysis, and we find the cumulative distribution functions of energy can be well fitted by bent power law and thresholded power law models. The distribution functions of fluctuations of energy well follow the Tsallis q-Gaussian distribution. The q values in the Tsallis q-Gaussian distribution are constant with small fluctuations for different temporal scale intervals, indicating a scale-invariant structure of the bursts. The earthquakes and soft gamma repeaters show similar properties, which are consistent with the predictions of self-organized criticality systems.
The second version of InRaDoS, a free computer program for internal dosimetry
Authors: Sadre Momtaz Alireza , Safarnejad Farzin
Published: December 2022

The calculation of absorbed and effective doses due to the administration of radiopharmaceuticals needs physical data such as radionuclide's half-life and nuclear decay data. Also, it needs the data on the biodistribution of the radiopharmaceutical in the body. This process is time-consuming, and there is a possibility of human error in the calculations. Therefore, computer programs were developed to facilitate and speed up the dose calculation. The purpose of this paper is to report the steps taken for the development of the second version of InRaDoS. InRaDoS 2 is a free computer program for internal dosimetry. This program was developed using the tkinter module of Python programming language. The dose calculations were based on the MIRD method and only for adults. The user can calculate the doses for revised ORNL or ICRP adult reference phantoms.
For now, 98 and 29 radiopharmaceuticals (138 and 42 biokinetic models) are available for the revised ORNL and ICRP adult reference phantoms, respectively. The results of the InRaDoS 2 show good agreement with the published data and free available software. InRaDoS 2 is freely available for download on GitHub
(https://github.com/farzinsafarnejad/InRaDoS-2).
Rapid expansion of irrigated agriculture in the Senegal River Valley following the 2008 food price crisis
Authors: Higginbottom Thomas P , Adhikari Roshan , Foster Timothy
Published: December 2022

The expansion of irrigated croplands throughout the 20th century boosted global agricultural productivity, yet limited improvement occurred in sub-Saharan Africa where many irrigation schemes and policies under-delivered. We mapped the distribution of croplands under active irrigation between 1986 and 2020 for one of Africa’s largest and most important transboundary river basins—the Senegal River Valley; using Landsat imagery with a random forest classifier and hidden Markov Model. We document two distinct epochs of irrigation development. Initially, a period of stagnation where less than 900 ha yr−1 was added, lasting until 2008. Followed by a boom phase of rapidly expanding intensively irrigated production with ∼9,000 ha yr−1 added for the last 12 years. These epochs overlap with national agricultural policy frameworks: the 1980s laissez-faire policies limited state involvement in agriculture and promoted Asian imports; followed by a more interventionist period focused on promoting domestic production following the food price crisis of 2008.
Local mode analysis of characteristic vibrational coupling in nucleobases and Watson–Crick base pairs of DNA
Authors: Quintano Mateus , Delgado Alexis A A , Moura Jr Renaldo T , Freindorf Marek , Kraka Elfi
Published: December 2022

Two-dimensional infrared spectroscopy has reported highly delocalized in-plane base vibrations in the fingerprint region of nucleotide monophosphates, suggesting the involvement of base pair C=O and C=C ring bonds and considerable interaction between C=O bond stretches. The high delocalization results in congested vibrational spectra, which complicates the assignment of the peaks. This congestion also extends to Watson–Crick base pairs. We applied in this work the characterization of normal mode procedure, a special feature of our local mode analysis, and could for the first time identify the C=O and C=C bonds being engaged in base pair coupling and quantify their contribution to each of the delocalized fingerprint vibration. In addition, a detailed and quantitative description of the hydrogen bonds involved in the Watson–Crick base pairs was provided. Based on the results of this study, we developed a new protocol to elucidate on the assignment of bands in the vibrational spectra of nucleic acids by probing the vibrational space for specific interactions between functional groups prior to and upon base pairing. This protocol will aid to fill the gap between deoxyribonucleic acid structural information and vibrational spectroscopy experiments by facilitating the interpretation of spectra on a quantitative basis.
Computational prediction and characterization of cell-type-specific and shared binding sites
Authors: Zhang Qinhu , Teng Pengrui , Wang Siguo , He Ying , Cui Zhen , Guo Zhenghao , Liu Yixin , Yuan Changan , Liu Qi , Huang De-Shuang
Published: December 2022

Motivation

Cell-type-specific gene expression is maintained in large part by transcription factors (TFs) selectively binding to distinct sets of sites in different cell types. Recent research works have provided evidence that such cell-type-specific binding is determined by TF’s intrinsic sequence preferences, cooperative interactions with co-factors, cell-type-specific chromatin landscapes and 3D chromatin interactions. However, computational prediction and characterization of cell-type-specific and shared binding sites is rarely studied.

Results

In this article, we propose two computational approaches for predicting and characterizing cell-type-specific and shared binding sites by integrating multiple types of features, in which one is based on XGBoost and another is based on convolutional neural network (CNN). To validate the performance of our proposed approaches, ChIP-seq datasets of 10 binding factors were collected from the GM12878 (lymphoblastoid) and K562 (erythroleukemic) human hematopoietic cell lines, each of which was further categorized into cell-type-specific (GM12878- and K562-specific) and shared binding sites. Then, multiple types of features for these binding sites were integrated to train the XGBoost- and CNN-based models. Experimental results show that our proposed approaches significantly outperform other competing methods on three classification tasks. Moreover, we identified independent feature contributions for cell-type-specific and shared sites through SHAP values and explored the ability of the CNN-based model to predict cell-type-specific and shared binding sites by excluding or including DNase signals. Furthermore, we investigated the generalization ability of our proposed approaches to different binding factors in the same cellular environment.

Availability and implementation

The source code is available at: https://github.com/turningpoint1988/CSSBS.

Supplementary information

Supplementary data are available at Bioinformatics online.
Randomized double-blind placebo-controlled crossover trial with pyridostigmine in spinal muscular atrophy types 2–4
Authors: Stam Marloes , Wijngaarde Camiel A , Bartels Bart , Asselman Fay-Lynn , Otto Louise A M , Habets Laura E , van Eijk Ruben P A , Middelkoop Bas M , Goedee H Stephan , de Groot Janke F , Roes Kit C B , Schoenmakers Marja A G C , Nieuwenhuis Edward E S , Cuppen Inge , van den Berg Leonard H , Wadman Renske I , van der Pol W Ludo
Published: December 2022

Hereditary proximal spinal muscular atrophy causes weakness and increased fatigability of repetitive motor functions. The neuromuscular junction is anatomically and functionally abnormal in patients with spinal muscular atrophy. Pharmacological improvement of neuromuscular transmission may therefore represent a promising additional treatment strategy. We conducted a Phase II, monocentre, placebo-controlled, double-blind, cross-over trial with the acetylcholinesterase inhibitor pyridostigmine in treatment-naïve patients with spinal muscular atrophy types 2–4. We investigated the safety and efficacy of pyridostigmine on fatigability and motor function. Each participant received pyridostigmine and a placebo for 8 weeks, in random order. Primary outcomes were the repeated nine-hole peg test for fatigability and motor function measure. Secondary outcomes were patient-reported effects, endurance shuttle test combined scores and adverse events. We included 35 patients. For the repeated nine-hole peg test, the mean difference was 0.17 s/trial (95% confidence interval: −1.17–1.49; P = 0.8), favouring placebo, and for the motor function measure, 0.74% (95% confidence interval: 0.00–1.49; P = 0.05), favouring pyridostigmine. Around 74% of patients reported medium-to-large beneficial effects of pyridostigmine on fatigability, compared with 29.7% in the placebo arm. This was paralleled by a reduced dropout risk of 70% on the endurance shuttle test combined scores (hazard ratio: 0.30; 95% confidence interval: 0.15–0.58) under pyridostigmine. Adverse events, mostly mild and self-limiting, occurred more frequently under pyridostigmine. No serious adverse events related to the study medication were observed. Patients with spinal muscular atrophy tolerated pyridostigmine well. There were no significant differences in primary outcomes, but the self-reported reduction of fatigability and improved endurance shuttle test combined score performance suggest that pyridostigmine may be useful as an additional therapy to survival motor neuron-augmenting drugs.

Trial registration number: EudraCT: 2011–004369-34, NCT02941328
fastball: a fast algorithm to randomly sample bipartite graphs with fixed degree sequences
Authors: Godard Karl , Neal Zachary P
Published: December 2022

Many applications require randomly sampling bipartite graphs with fixed degrees or randomly sampling incidence matrices with fixed row and column sums. Although several sampling algorithms exist, the ‘curveball’ algorithm is the most efficient with an asymptotic time complexity of $O(n~log~n)$ and has been proven to sample uniformly at random. In this article, we introduce the ‘fastball’ algorithm, which adopts a similar approach but has an asymptotic time complexity of $O(n)$. We show that a C$\texttt{++}$ implementation of fastball randomly samples large bipartite graphs with fixed degrees faster than curveball, and illustrate the value of this faster algorithm in the context of the fixed degree sequence model for backbone extraction.
Regulation at Drosophila’s Malic Enzyme highlights the complexity of transvection and its sensitivity to genetic background
Authors: Rzezniczak Teresa Z , Rzezniczak Mark T , Reed Bruce H , Dworkin Ian , Merritt Thomas J S
Published: December 2022

Transvection, a type of trans-regulation of gene expression in which regulatory elements on one chromosome influence elements on a paired homologous chromosome, is itself a complex biological phenotype subject to modification by genetic background effects. However, relatively few studies have explored how transvection is affected by distal genetic variation, perhaps because it is strongly influenced by local regulatory elements and chromosomal architecture. With the emergence of the “hub” model of transvection and a series of studies showing variation in transvection effects, it is becoming clear that genetic background plays an important role in how transvection influences gene transcription. We explored the effects of genetic background on transvection by performing two independent genome wide association studies (GWASs) using the Drosophila genetic reference panel (DGRP) and a suite of Malic enzyme (Men) excision alleles. We found substantial variation in the amount of transvection in the 149 DGRP lines used, with broad-sense heritability of 0.89 and 0.84, depending on the excision allele used. The specific genetic variation identified was dependent on the excision allele used, highlighting the complex genetic interactions influencing transvection. We focussed primarily on genes identified as significant using a relaxed P-value cutoff in both GWASs. The most strongly associated genetic variant mapped to an intergenic single nucleotide polymorphism (SNP), located upstream of Tiggrin (Tig), a gene that codes for an extracellular matrix protein. Variants in other genes, such transcription factors (CG7368 and Sima), RNA binding proteins (CG10418, Rbp6, and Rig), enzymes (AdamTS-A, CG9743, and Pgant8), proteins influencing cell cycle progression (Dally and Eip63E) and signaling proteins (Atg-1, Axo, Egfr, and Path) also associated with transvection in Men. Although not intuitively obvious how many of these genes may influence transvection, some have been previously identified as promoting or antagonizing somatic homolog pairing. These results identify several candidate genes to further explore in the understanding of transvection in Men and in other genes regulated by transvection. Overall, these findings highlight the complexity of the interactions involved in gene regulation, even in phenotypes, such as transvection, that were traditionally considered to be primarily influenced by local genetic variation.
Variations of stomata development in tea plant (Camellia sinensis) leaves in different light and temperature environments and genetic backgrounds
Authors: Li Ping , Lin Junming , Zhu Mingzhi , Zuo Hao , Shen Yihua , Li Juan , Wang Kunbo , Li Penghui , Tang Qian , Liu Zhonghua , Zhao Jian
Published: December 2022

Stomata perform important functions in plant photosynthesis, respiration, gas exchange, and interactions with environments. However, tea plant stomata development and functions are not known. Here, we show morphological changes during stomata development and genetic dissection of stomata lineage genes regulating stomata formation in tea developing leaves. Different tea plant cultivars displayed clear variations in the stomata development rate, density and size, which are closely related to their tolerance against dehydration capabilities. Whole sets of stomata lineage genes were identified to display predicted functions in regulating stomatal development and formation. The stomata development and lineage genes were tightly regulated by light intensities and high or low temperature stresses, which affected stomata density and function. Furthermore, lower stomatal density and larger size were observed in triploid tea varieties as compared to those in diploid plant. Key stomata lineage genes such as CsSPCHs, CsSCRM, and CsFAMA showed much lower expression levels, whereas negative regulators CsEPF1 and CsYODAs had higher expression levels in triploid than in diploid tea varieties. Our study provides new insight into tea plant stomatal morphological development and the genetic regulatory mechanisms on stomata development under abiotic stresses and genetic backgrounds. The study lays a foundation for future exploring of the genetic improvement of water use efficiency in tea plants for living up to the challenge of global climate change.
Teaching/Learning through “Black Earth Rising”: Poststructural, Decolonial, and Feminist Readings
Authors: Cuadro Mariela
Published: December 2022

The paper aims at reflecting on ways of teaching/learning international relations (IR) critical theories. It does so by analyzing the results of a teaching/learning exercise based on Netflix's series “Black Earth Rising” and put into practice with undergraduate students of a course on IR theory taught at the Argentinian Universidad Nacional de San Martín. Assuming that series of mass consumption work as cultural devices that inform power relations through the production of truths and subjectivities, the exercise had two main objectives: on the one hand, to develop and illustrate otherwise difficult-to-grasp concepts of IR theory and, on the other hand, to make the students aware of how widespread TV series participate in the constitution of both international politics and their own subjectivities.
Preoperative serum interleukin-6 level in head and neck cancer reflects systemic inflammatory response and is a predictor of postoperative prognosis
Authors: Imai Takayuki , Nakamura Kazuki , Morita Sinkichi , Hasegawa Kohsei , Goto Takahiro , Katori Yukio , Asada Yukinori
Published: December 2022

Background

The outcome of head and neck cancer has improved in recent years but survival is not yet satisfactory. Interleukin (IL)-6 is a representative inflammatory cytokine and inducer of systemic inflammatory response. It is not known whether preoperative serum level of IL-6 is a prognostic factor in head and neck cancer surgery.

Methods

We studied 181 consecutive patients who underwent head and neck surgery with free tissue transfer reconstruction (HNS-FTTR) between September 2016 and December 2020. Whether preoperative serum IL-6 level was a prognostic risk factor was retrospectively investigated by univariate and multivariate analyses. We also investigated the association between preoperative IL-6 level and representative systemic inflammatory response markers.

Results

The preoperative IL-6 ≥ 8 pg/mL group had a significantly worse prognosis than the preoperative IL-6 < 8 pg/mL group (overall survival [OS]: hazard ratio [HR] 3.098, P = 0.0006; disease-specific survival [DSS]: HR 3.335, P = 0.0008). In multivariate analysis, IL-6 ≥ 8 pg/mL and age ≥ 70 years were independent poor prognostic factors for OS (HR 1.860, P = 0.0435 and HR 1.883, P = 0.0233, respectively). The only independent poor prognostic factor for DSS was IL-6 ≥ 8 pg/mL (HR 2.052, P = 0.0329). Serum albumin was significantly lower and serum C-reactive protein and neutrophil-to-lymphocyte ratio were significantly higher in the IL-6 ≥ 8 pg/mL group than in the IL-6 < 8 pg/mL group (all P < 0.0001).

Conclusions

Preoperative serum IL-6 level is an independent poor prognostic factor for both OS and DSS after HNS-FTTR, reflecting the degree of preoperative systemic inflammatory response.