bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamics analysis and cryptographic implementation of a fractional-order memristive cellular neural network model
Authors: Zhou 周 Xinwei 新卫 , Jiang 蒋 Donghua 东华 , Nkapkop Jean De Dieu , Ahmad Musheer , Fossi Jules Tagne , Tsafack Nestor , Wu 吴 Jianhua 建华
Published: October 2023

Due to the fact that a memristor with memory properties is an ideal electronic component for implementation of the artificial neural synaptic function, a brand-new tristable locally active memristor model is first proposed in this paper. Here, a novel four-dimensional fractional-order memristive cellular neural network (FO-MCNN) model with hidden attractors is constructed to enhance the engineering feasibility of the original CNN model and its performance. Then, its hardware circuit implementation and complicated dynamic properties are investigated on multi-simulation platforms. Subsequently, it is used toward secure communication application scenarios. Taking it as the pseudo-random number generator (PRNG), a new privacy image security scheme is designed based on the adaptive sampling rate compressive sensing (ASR-CS) model. Eventually, the simulation analysis and comparative experiments manifest that the proposed data encryption scheme possesses strong immunity against various security attack models and satisfactory compression performance.
Studies about zones of proximal mathematical development and methods of developmental teaching of Mathematics
Authors: Semenets S P , Semenets L M , Andriichuk N M , Chugunova O V , Lutsyk O M
Published: October 2023

The work develops the doctrine of the zones of the nearest mathematical development in the education seekers, reveals their content, substantiates the classification basis, and establishes typological characteristics. The structural and functional features of the studied phenomenon are represented by the principle of developmental continuity of Mathematics education and the task structure of educational and mathematical activities. In this way, compliance with the deductive essence of Mathematics was ensured, and emphasis was also placed on the phenomenological characteristics of mathematical abilities – the ability to generalize the content of mathematical education. Taking into account the established zones of the nearest mathematical development of the students of education, using the system approach and the modeling method, a theoretical-probabilistic methodical model of the developmental teaching of Mathematics was built, and the content of its stages was revealed. It was established that the method of developmental teaching of Mathematics involves the following stages: determination of areas of actual mathematical development; creation of areas of proximal mathematical development; transformation of zones of the nearest mathematical development into zones of actual mathematical development; designing the zones of the nearest mathematical development in the education seekers. Taking into account the problem raised in the work, the results of a pilot study on the manifestations of mathematical abilities of education seekers, significant factors of their development, as well as the effectiveness of the methodology of developmental teaching of Mathematics were experimentally verified.
Methodology of project-based learning for training junior students in applied mathematics: general scheme of the educational process
Authors: Akhiiezer O B , Haluza O A , Savchenko A O , Lyubchyk L M , Protsay N T , Aslandukov M O
Published: October 2023

An original methodology of the project-based learning for junior students of the specialty applied mathematics is proposed in the paper. A complete step-by-step diagram (as a BPMN diagram) of the process of the project-based learning as a business process with a description of the specific actions of all its participants is given. The paper specified and clearly describes all the main aspects of the work on the project, starting from the criteria that the project problem must satisfy, and ending with the form of project defense. The roles of both students within the project team and all teachers are described in detail. Special attention is paid to all documents accompanying the work on the project, which should be submitted by the project team. The results of the article may be useful to those teams of teachers who are just starting to work on the implementation of project-based learning into the educational process for the specialty of applied mathematics or related ones.
Measuring Earth’s mean density using BYOD technology
Authors: Zdeshchyts A V , Zdeshchyts V M
Published: October 2023

BYOD (Bring your own devices) technologies are becoming more relevant in the educational process, when equipment that is “in the pocket” of a modern student is used in classes. BYOD technology becomes most effective if all students are provided with research equipments. But it is difficult to ensure such conditions in terms of distance learning during the war, the coronavirus pandemic, etc. In order to solve this problem, it is necessary to be able to develop laboratory installations that each student can make on his own. As an example of the implementation of this principle, the article considers a physical installation and a method of conducting laboratory work: “Measuring Earth’s mean density using BYOD technology”, which allows physics students, geodesists, surveyors to determine for themselves that the Earth has a heavy core. The purpose of this article is to show that a smartphone is a powerful measurement tool that, in combination with BYOD technology, increases student learning opportunities, namely: makes laboratory practice not too difficult; provides an opportunity to conduct experiments both in the laboratory and remotely. The main result of the work is proving the fact that the use of BYOD technology in combination with modern measuring tools – smartphones equipped with appropriate applications allows (to solve) the problem of distance learning of students. As it shown by the results of measuring the Earth’s mass and density using BYOD technology, the values are consistent with the known ones obtained with more difficult to use and expensive technique. Along with the values of mass and density, the student receives other characteristics of the Earth: the value and slope of the induction vector of its magnetic field. Exceeding of the Earth’s mean density, which is equal to 5676 kg/m3 according to the results of experiments; the density of the main rock-forming minerals in the Earth’s crust, which is in the range of 1900-3500 kg/m3, leads the student-researcher to think about the internal structure of the Earth.
Using open experimental data of the European Organization for Nuclear Research in the process of studying the physics of elementary particles
Authors: Kukharchuk R P , Vakaliuk T A , Zaika O V , Riabko A V , Medvediev M G
Published: October 2023

The article discusses the theoretical justification, and the process of developing, implementing, and experimentally verifying the methodology for training future physics teachers using open experimental data from the European Center for Nuclear Research in studying elementary particle physics. The main stages of the study of elementary particle physics are clarified, taking into account the modern achievements of CERN. In the work, the study of elementary particles was carried out based on data from the CMS detector (Compact Muon Solenoid). A description of the methods, techniques, and ways of using the proposed methodological tools for the workshop on the physics of the atomic nucleus and elementary particles is presented. The process of selection and preparation of tasks and instructions based on the open experimental data of the European Center for Nuclear Research, recommendations for working with software, and their approbation in the educational process is considered. An experimental verification, analysis, and generalization of the research results were carried out. Arguments are given regarding the effectiveness and practicality of using the open experimental data of CERN in the process of studying elementary particle physics.
Design and fabrication of an improvised Young’s Modulus Apparatus
Authors: Patero J L
Published: October 2023

In elasticity of matter, the behaviour of elastic materials are described in terms of elongation, external force applied to elastic materials, stress, strain, and elastic moduli such as Young’s modulus, Shear modulus, and Bulk modulus. Demonstration of this elastic modulus, particularly Young’s modulus in the classroom is a usual problem because acquiring an apparatus for this purpose is expensive. In this paper, improvised Young’s modulus apparatus is fabricated. The improvised Young’s modulus apparatus is tested using pure copper wire, and two other metallic wires of stainless steel and galvanized iron wires: the copper wire of diameter 0.42 mm has a Young’s modulus of 10.04 × 1010 N/m2 ± 6.783 N/m2 which is 8.7% than the known Young’s modulus of pure copper wire. On the other hand, the Young’s modulus of GI wire of diameter 0.555 mm and stainless steel wire of diameter 0.42 mm are 17.92 × 1010 N/m2 and 18.021 × 1010 N/m2, respectively. The improvised apparatus is functional and can be used for classroom experiments and demonstration.
Modeling training content for software engineers in parallel computing
Authors: Sitsylitsyn Y O , Osadchyi V V , Kruglyk V S , Kuzminska O H
Published: October 2023

This study proposes a robust framework for the training of software engineers specializing in parallel computing. We first curated essential content for parallel computing education based on international standards and evolving recommendations from Computing Curricula. We then systematically structured the content and designed a well-defined learning pathway for aspiring software engineers. Concurrently, we conducted a comprehensive assessment of the current state of training for parallel computing in Ukrainian higher education institutions. We analyzed bachelor’s programs in Information Technologies and scrutinized individual course syllabi to identify valuable insights. By merging our findings with the review of educational programs, we formulated a comprehensive model for training in parallel computing. We also examined the pivotal role of the course ”Parallel and Distributed Computing” in the developed curriculum and identified essential tools and methodologies for developing parallel and distributed programs. Our research contributes to the advancement of parallel computing education and provides a valuable reference point for curriculum designers and educators.
Understanding and attitude toward upcycling according to the survey of students of various specialities
Authors: Derkach T M , Bilianska M M , Yaroshenko O G
Published: October 2023

The attitude to upcycling technologies of undergraduate students of five specialities (design, clothing industry technology, vocational education and training, industrial pharmacy and psychology) and their teachers was investigated using the questionnaire method. Students’ pReferences practically do not depend on specialities. For all students, subgroups of upcycling enthusiasts and sceptics are observed which regularly resort to upcycling or almost do not use it. An almost complete misunderstanding and imperception of the benefits and importance of upcycling is a key and common problem. Social factors have a minimal influence on the opinion of respondents, which may indicate a lack of understanding in society of the role and importance of waste management. All the shortcomings and problems in understanding upcycling are common to students and teachers. In general, the positive attitude towards upcycling and the intention to use upcycling in life in the answers most likely has an unconscious and artificial character (like a fashion trend) because the attitude towards other formative factors does not support it. The identified problems are related to the shortcomings of secondary school and undergraduate curricula, which hinder the formation of the necessary competencies for sustainable development. Methods of their solution are proposed and discussed.
Design of Electric Vehicle Battery Management System
Authors: Liu Qian , Chen Gang
Published: October 2023

The Battery Management System (BMS) is a fundamental component of electric vehicles, primarily utilized to ensure battery safety and enhance battery lifespan. This article presents a design for both the hardware and software components of the BMS, enabling battery monitoring and management. The hardware component encompasses the design of voltage acquisition circuitry, second-order filtering circuitry, sampling and holding circuitry, CAN bus communication circuitry, and other relevant features. The software section comprises subroutines for battery information collection, equalization circuitry, SOC estimation, and other relevant features. The BMS developed in this study successfully collects voltage, temperature, current, and other relevant information, and accurately estimates SOC and other crucial parameters. Testing confirmed that the battery management system precisely collects battery voltage, current, and temperature information, while the SOC estimation achieves a relatively high degree of accuracy.
Research on the design of direct-drive permanent magnet generator for hybrid UAV
Authors: Zhang Weihao , Han Pengfei , Peng HaiTao , Yang Ling
Published: October 2023

As the core of the power system, the performance of the generator is crucial to the flight and operation of the drone. This paper introduces the design and research of a direct-drive permanent magnet generator for gasoline-electric hybrid UAV. A computationally efficient optimization design method was proposed, and the generator used in the 25 kg UAV was designed
Construction of a 3D Distribution Network Environment Based on Multi-source Data Fusion
Authors: Li Xiayang , Li Xiang , Li Zhaoyu , Huang Zeyi , Kang Haiyun , Ma Haixia
Published: October 2023

Traditional distribution networks are designed using two-dimensional drawings. Its expression is abstract, the accuracy of manually measured elevation data could be higher, and complex sections are difficult to measure. To solve this problem, a three-dimensional environment for digital planning and design of the distribution network is proposed by combining laser point cloud and oblique photography modelling. Firstly, a rough registration method based on the main material plane is proposed to improve the registration efficiency. The GICP method is used to accurately register the point cloud and build a refined model of distribution equipment; Then, the UAV tilt photography technology is used to model the distribution line corridor, and the elevation model is obtained at the same time. The experimental results show that the model error after precise registration is 3.75 cm, which meets the requirements of high-precision modelling. The average error between the elevation model obtained by the tilt photography of the distribution line corridor and the measured elevation is 0.112 m, which meets the accuracy requirements of mapping.
Machining Characteristics of High-gradient Inside Surface Using Long Tool Holder
Authors: Wang Guilin , Tang Li , Lai Tao , Li Xincai
Published: October 2023

In order to meet the requirements of space reachability, the high-gradient inside surfaces such as infrared optical domes need to be machined with a long tool holder. Under the action of lateral cutting force, the long tool holder is easy to chatter, and the machined surface will roughen. The directionality of cutting force and its influence on chatter marks are studied in the machining process of high-gradient inside surface, and the dynamic model on tool holder is built in this paper. The natural frequency increases to 2820Hz for long tool holder by optimizing its structure and the clamping method, and the dynamic characteristics is greatly improved. The surface roughness is better than Ra 3.3nm for thermocompressed polycrystalline MgF2 parts which are machined in different directions, there aren’t chatter marks on the surface, and the machining requirements are satisfied for infrared optical parts.
A Three-element Risley Prism Continuous Scanning System Based on Linear Constraint
Authors: He Xiaodong , Che Guohua , Li Hualian , Si Jianwei
Published: October 2023

In the three-element Risley prism system, non-linear errors, the infinite solution, the blind zone and the singularity are primary factors that affect the scanning accuracy of the system. In this paper, an accurate analytical model of the three-element Risley prism system is proposed. To reduce the errors of single-wedge nonlinear constraint equation, a dimensionality reduction method constrained by a single wedge is adopted. In addition, a reliable accuracy of 5mm is employed to achieve a full-area scanning of the system, and a single wedge linear constraint equation with an angular increment is established to control singularities. Simulation results show that the wedge rotation angle curve is stable and continuous in the process of inverse solution, and the full coverage of the scanning area can be achieved by assigning scanning accuracy to 5mm, which indicates that the proposed method can effectively solve the problems and achieve full-area scanning in the system.
Research on Decoupling of Fiber Bragg Grating Tactile Signal Based on Neural Network
Authors: Yan Haitang , Jin Rencai , Zhang Jiaojiao , Qian Yuandi , Qian Muyun
Published: October 2023

For the purpose of resolving the nonlinear coupling problem of the three-dimensional force of the fiber Bragg grating tactile sensor applied to flexible wearable devices, we propose a method to decouple the three-dimensional force signal by applying the error back-propagation neural network and the radial-based neural network to simulation and experiment based on the mechanical finite element simulation of the sensing unit, using the fiber Bragg grating tactile sensor as the research object. The decoupling results of the neural network on the 3D force simulation data show that the radial-based neural network has higher decoupling accuracy than the error back-propagation neural network, and can better approximate the mapping relationship between the 3D force magnitude containing noise and the center wavelength drift of the FBG tactile sensor. The research results of this paper are of practical value for the research and promotion of the flexible haptic sensor for electronic skin.
Algorithm for Enhancing the Resolution of Workshop Part Images
Authors: Hua Jiyong , Yin Hongmei , Li Zhijun , Wang Shaojun , Chen Chen
Published: October 2023

The resolution of the input image will affect the restoration effect of the image. In a fixed environment, obtaining high-quality images requires expensive acquisition devices, such as cameras. There are many ways to improve image quality. Instead of increasing hardware investment, it is better to find methods in image post-processing. Deep learning algorithms have obvious advantages in image processing. Based on deep learning, we propose an algorithm to convert camera captured images into high-resolution images. VDSR (Very Accurate Super Resolution) is a typical algorithm. Use residual image learning to predict accurate residual images from input images. Residual corresponds to the high-frequency information in an image, representing pixels that undergo drastic changes in the image, and can highlight the edges and contours of the target. Our proposed algorithm is more accurate than existing algorithms and improves visual effects.
Simulation of Beamline Motion Control System of Shanghai Synchrotron Radiation Facility BL13U
Authors: Liu Yuhao , Zhao Ying , Zheng Lifang , He Yan , Li Aiguo
Published: October 2023

The Shanghai Synchrotron Radiation Facility’s hard X-ray nanoprobe wire station is currently under construction, so it is unable to conduct research on online testing, however, beamline adjustment is crucial prior to conducting experiments at the wire station, this challenge can be more effectively addressed by using simulation testing instead of online testing. In order to carry out intelligent beamline adjusting research before the online station is completed, this paper designs a beamline adjusting test simulation platform based on the EPICS software. Through the software simulation of the motor control system of the above-mentioned beamline, the beamline adjusting application of intelligent control methods is realized. The test results show that the system runs well and the intelligent beamline adjusting algorithm can efficiently and automatically optimize the motors in the system. The beamline adjusting test platform based on EPICS software can be further applied to the simulation and testing of other beamlines at the Shanghai Synchrotron Radiation Facility.
Study on Deformation Mechanism of Saturated Sand Based on Discrete Element Method
Authors: Wang Xiaoli , Xu Chengshun , Jiang Chenglong , Zhang Xiaoling
Published: October 2023

Based on the discrete element program (particle flow code PFC3D), the effects of the initial void ratio on the macroscopic and microscopic mechanical responses, phase transition state and critical state characteristics of saturated sand are systematically investigated in drained tests. The phenomenon that saturated sand enters the critical state earlier than the laboratory macroscopic results is revealed from the microscopic point of view. The results show that the phase transition state of the saturated sand can be reflected by the extreme values of void ratio, sliding ratio, suspended particle ratio and mechanical coordination number. Compared to the macroscopic parameters stress ratio and volume strain, the microscopic parameters can earlier reveal the critical state of saturated sand. The saturated sands with different initial void ratios have the same anisotropy component at the critical state. At the phase transition state, only the weight of normal contact force anisotropy is in the peak state. During the development of saturated sand from shrinkage to dilatancy, the velocity of particle motion on the diagonal 45° shear surface of the sample is intense and the particle motion is dominated by rotation. The above conclusions expand the current understanding of the deformation mechanism at the phase transition state and critical state of the soil.
Biologically inspired virtual aperture extension method of small aperture HFSWR multielement array
Authors: Li Hongbo , Liu Aijun , Yang Qiang , Yu Changjun , Yang Xuguang
Published: October 2023

We propose a method for extending the virtual aperture of the small aperture high-frequency surface wave radar multielement array inspired by a fly named Ormia ochracea. Despite the tremendous incompatibility between its ear and the incoming wavelength, Ormia can accurately local the sound of its host cricket. This ability benefits from the coupled structure of Ormia’s ears which have been modelled as a mechanical vibration system. In this paper, we first design a two-degree of freedom biologically inspired coupled system by mimicking Ormia’s coupled ears. We quantitatively analyze its extension capability to the array aperture and construct the received signal model of the virtual array. We then analyze its response characteristic and available frequency band. To achieve the applications of arbitrary desired frequencies, we propose a frequency conversion algorithm. Moreover, we design two multi-degree of freedom biologically inspired coupled systems for the multielement array We summarize the criteria for extending the degree of freedom and optimize these two systems to address their respective shortcomings. Numerical results give the optimal system parameters for our desired frequency and validate the frequency conversion algorithm. By comparing the radiation pattern of the inspired arrays (arrays with the proposed systems) with that of an ordinary array, we demonstrate the virtual aperture extension capability of our proposed method. We also verify the effectiveness of proposed method by processing the actual received signals of the array.
Investigating the occurrence of blizzard events over the contiguous United States using observations and climate projections
Authors: Browne Ahmani , Chen Liang
Published: October 2023

Over previous decades, the United States has been plagued by severe winter storms or blizzards, which caused millions of dollars in damages. However, the historical trend of blizzard events and the possible impacts of future global climate change on blizzard occurrences remain unclear. In this study, we analyzed historical blizzard occurrences using the observed storm event database, which shows that the Northern Plains, such as North Dakota, South Dakota, and Minnesota, had the most blizzard activities over the past 25 years. No significant trend in blizzard occurrence is found in those regions. When considering blizzards as compound events of strong wind and extreme snowfall, we estimated blizzard occurrences based on wind speed and snowfall in climate datasets, including Automated Surface Observing Systems wind speed, national gridded snowfall analysis, ERA5 reanalysis and historical simulations of 19 models in Coupled Model Intercomparison Project phase 6 (CMIP6), which show a good agreement with the observations with respect to the climatology of blizzard occurrence. In the near-term and long-term future under two emission scenarios, CMIP6 projections suggest decreases in both strong wind and extreme snowfall events, eventually leading to a significantly reduced frequency of compound events. Significant decreases in blizzard occurrence are found in the Northern Plains and Upper Midwest, suggesting potentially reducing the risk of winter hazards over those regions in a warming climate.
Design of a wideband and tunable radar absorber
Authors: Gao Xin , Dou Zheng , Peng Ruihui , Wang Xiangwei , Lv Yongsheng
Published: October 2023

To effectively address the challenges posed by intricate and dynamic electromagnetic environments, we propose a wideband and tunable radar absorber in this paper. The proposed absorber, composed of graphene capacitor, plasma enclosed within a sealed glass cavity, radar absorbing material (RAM), FR-4 and copper plate, allows for tunable radar absorbing performance through the manipulation of the electromagnetic properties of the graphene capacitor and plasma. Based on the equivalent circuit model, the reflectivity of the radar absorber is analyzed using transmission line theory (TLT). Good agreement is observed between the full-wave simulations and the TLT. The study thoroughly investigates the influence of graphene, plasma, and RAM components, as well as their sequential arrangement within the radar absorber, on its reflectivity, expounding the fundamental mechanism of these materials’ synergistic integration. Additionally, the effects of key factors, including the surface resistance R

g
of graphene, plasma frequency

w

p

,

collision frequency

v

p

and plasma thickness

t

plasma

,

on the radar absorbing performance are examined. Our findings reveal that adjusting surface resistance R

g
controls the absorbing amplitude, and manipulation of the plasma frequency and collision frequency tunes the absorbing frequency and effective absorbing band. By appropriately adjusting the surface resistance R

g
of graphene, plasma frequency

w

p

and collision frequency

v

p

,

the proposed radar absorber exhibits superior performance in the frequency range of 1 GHz to 10 GHz. The radar absorber we propose serves as a significant reference for the application of tunable radar absorbers and adaptive radar stealth techniques.
Reactively-sputtered super-hydrophilic ultra-thin titania films deposited at 120 °C
Authors: Kaidatzis Andreas , Mouti Nafsika , Arfanis Michalis , Papadimitropoulos Giorgos , Mitterer Christian , Falaras Polycarpos , Giannakopoulos Konstantinos
Published: October 2023

We investigate super-hydrophilic TiO2 (titania) films for concentrated solar-thermal power applications. Reactive magnetron sputtering has been used to deposit 8 to 12 nm thick titania thin films onto borosilicate microscope glass slides, low-Fe extra-clear architectural glass, or Si(100) wafers with a 500 nm thick thermal SiO2 layer. The effects of deposition temperature and O2 fraction of the O2/Ar working gas were investigated. We demonstrate the importance of the O2 fraction for obtaining optically transparent, super-hydrophilic (contact angle below 1°) thin films. In particular, we show that as the O2 fraction increases, contact angle decreases, obtaining super-hydrophilic titania thin films at deposition temperatures as low as 120 °C. Our work enables to develop low thermal budget cost-efficient industrial synthesis processes, paving the way for commercial applications.
Revealing the changes in water footprint at the provincial level and their drivers in the Yellow River Basin, China
Authors: Xia Qing , Tian Guiliang , Hu Hao , Wu Zheng
Published: October 2023

Water scarcity has become the most significant limiting factor for sustainable economic and social development in the Yellow River Basin (YRB). Despite this, most current studies on water resources in the YRB from a water footprint (WF) perspective have focused on WF measurements and have explored the influencing factors of WF changes in certain industries, while the impact mechanisms driving regional WF changes remain unclear. To bridge this research gap, the WF of nine provinces in the YRB for 2012 and 2017 were quantified using an environmentally extended multi-regional input-output model (EE-MRIO), and the driving forces of regional WF changes were explored via structural decomposition analysis (SDA). The results showed that the WF of the YRB increased by 3.8% to 113.64 billion m3 between 2012 and 2017. With rapid economic development and enhanced inter-regional trade links, the external WF has played an important role in meeting local water demand. Technological advances and production structure adjustments contribute to the reduction of the WF, thus promoting the sustainable use and management of the YRB’s water resources. Both consumption patterns and final demand per capita have dominated the YRB’s WF growth, particularly in the economically developed middle and lower reaches, where urban household consumption drove the largest WF, accounting for over 40%. Therefore, in the future, continuous optimization of the consumption structure and guidance of green consumption awareness are expected to contribute more to the reduction in WF. The findings of this study reveal the primary causes of WF changes in the YRB and offer a theoretical justification for the formulation of water conservation and sustainable utilization policies.
Egyptology and African History
Authors: Moreno García Juan C.
Published: October 2023

Egyptology has played a rather ambiguous role in the study of the African past. While the Nile Valley was the cradle of one of the oldest states as well as of crucial innovations like writing, monumental architecture, and complex administrative managerial techniques, among others, the burden of Eurocentric historiographical prejudices considered these achievements to be a sort of anomaly. Ancient Egypt was thus interpreted through the lens of an alleged “exceptionalism”—a geographically African but, quite self-contradictorily, culturally non-African society. Such a view was rooted in a too-literal reading of pharaonic texts and images that celebrated the differences between Egypt and its neighbors. At the same time, Egypt was seen as a remote precedent of Western culture and societies—a venerable instigator of an uninterrupted process of progress supposedly culminating in Europe in the 19th century. Only as of the late 20th century has archaeology helped Egyptology overcome such a view, understand the African roots of the pharaonic civilization, and review the nature of its relations with its African neighbors. At the same time, intense archaeological exploration of the African regions that surrounded Egypt has revealed the critical role of Nubian and desert populations in creating original forms of political power and cultural achievement that owed little or nothing to pharaonic Egypt. The result is the emergence of more balanced historical interpretations that emphasize the complex interplay between all these actors in the social dynamics of the Bronze and Iron Age in northeastern Africa.
Peer Effects in Education
Authors: Barrios-Fernandez Andrés
Published: October 2023

The identification of peer effects is challenging. There are many factors not related to social influences that could explain correlations among peers. Peers have been shown to affect many important outcomes, including academic performance and educational trajectories. Confirming the existence of peer effects is important from a policy perspective. Both the cost-benefit analysis and the design of policies are likely to be affected by the existence of social spillovers. However, making general policy recommendations from the current evidence is not easy. The size of the peer effects documented in the literature varies substantially across settings and depends on how peers are defined and characterized. Understanding what is behind this heterogeneity is thus key to extract more general policy lessons. Access to better data and the ability to map social networks will likely facilitate investigating which peers and which characteristics matter the most in different contexts. Conducting more research on the mechanisms behind peer effects is also important. Understanding these drivers is key to take advantage of social spillovers in the design of new educational programs, to identify competing policies, and to gain a deeper understanding of the nature and relevance of different forms of social interactions for the youth.
Strategic Use of Law in Global Politics
Authors: Reed Kyle
Published: October 2023

Although international law is often understood as a system of restraint—rules meant to constrain what states or other actors may do—attention has increasingly shifted to its use as a strategic tool. Actors often employ international legal references and claims in support of their policy decisions. Law’s status as a unique type of social norm, one that reflects supposedly neutral and agreed-upon rules, gives it a unique place in international politics, which actors may benefit from through the strategic use of international law and legal references in different political arenas. Understanding the place of international law in politics, then, requires understanding how, why, and when actors strategically use it and to what effects. In response to these questions, international relations scholarship has begun to develop new theories to better understand the use of international law in politics—why actors employ it and what makes it effective. This combines insights from rationalist approaches to politics—highlighting the role law can play as a coordination device—with more constructivist ideas on discourse and identity. By identifying the different actors who use international law, and the varied ways in which it can and is employed for strategic purposes, scholarship engages with questions of legalization but also the broader place of law in politics. Simultaneously, scholars have turned their attention to the use of law in different areas of politics. This has set the stage for further scholarship not only on the use of law, or the effect of these uses on political outcomes, but also on the relationship between such strategic uses of law and the meaning and place of the law itself.
Earthen Tumuli Archaeology in West Africa
Authors: Magnavita Sonja
Published: October 2023

Earthen tumuli are a special type of grave that is widespread all over the world. In West Africa, they belong to a type of monument that attracted archaeological interest at the turn of the 20th century. West African burial mounds underwent the greatest wave of archaeological excavations in the first half of the 20th century, but owing to difficult excavation conditions and technical-logistical challenges on the one hand and an increasing interest in the study of prehistoric settlement and economy on the other, attention to earthen tumuli research declined significantly in the second half of the 20th century. In the early 21st century, burial mounds are understood as representative individual or collective tombs that may offer insight into the social structure—or what was intended to be mediated by it—of part of the late prehistoric and early historic society in diverse regions of West Africa. However, an integration of archaeological evidence on particular funerary monuments such as tumuli with simpler graves for the general community and the living, crafting, and economic activities of everyday life has yet to occur in West African archaeology.
The phenotypic and genotypic association of grip strength with frailty, physical performance and functional limitations over time in older adults
Authors: Stringa Najada , van Schoor Natasja M , Hoogendijk Emiel O , Milaneschi Yuri , Huisman Martijn
Published: October 2023

Objectives

To replicate the phenotypic associations of grip strength with frailty, physical performance and functional limitations in older adults for longer follow-up periods and to examine whether these associations are due to shared genetic factors.

Methods

In total 2,262 participants 55 years and older with follow-up data up to 23 years (Nobservations = 8,262) from the Longitudinal Aging Study Amsterdam were included. Weighted polygenic risk scores for grip strength (PRS-GS) were built using the genome-wide meta-analysis results from UK Biobank as reference. Grip strength was measured two times on each hand using a dynamometer. Frailty index (FI) and frailty phenotype were operationalised following standard procedures. Performance tests included a timed walk test, a repeated chair stands test and put on–take off cardigan test. Functional limitations were assessed using a questionnaire with six items.

Results

Higher grip strength was phenotypically associated with lower FI (b = −0.013, 95% CI (−0.016, −0.009)), better physical performance (b = 0.040, 95% CI (0.026, 0.054)) and less functional limitations (OR = 0.965, 95% CI (0.954, 0.977)) over time for follow-up periods up to 23 years. However, PRS-GS was not associated with any of the traits.

Conclusion

The phenotypic associations between grip strength, frailty, physical performance and functional limitations were replicated for follow-up periods up to 23 years. However, the associations between the traits could not be explained by shared genetics potentially indicating a more relevant involvement of non-genetic factors.
NetAllergen, a random forest model integrating MHC-II presentation propensity for improved allergenicity prediction
Authors: Li Yuchen , Sackett Peter Wad , Nielsen Morten , Barra Carolina
Published: October 2023

Motivation

Allergy is a pathological immune reaction towards innocuous protein antigens. Although only a narrow fraction of plant or animal proteins induce allergy, atopic disorders affect millions of children and adults and cost billions in healthcare systems worldwide. In silico predictors can aid in the development of more innocuous food sources. Previous allergenicity predictors used sequence similarity, common structural domains, and amino acid physicochemical features. However, these predictors strongly rely on sequence similarity to known allergens and fail to predict protein allergenicity accurately when similarity diminishes.

Results

To overcome these limitations, we collected allergens from AllergenOnline, a curated database of IgE-inducing allergens, carefully removed allergen redundancy with a novel protein partitioning pipeline, and developed a new allergen prediction method, introducing MHC presentation propensity as a novel feature. NetAllergen outperformed a sequence similarity-based BLAST baseline approach, and previous allergenicity predictor AlgPred 2 when similarity to known allergens is limited.

Availability and implementation

The web service NetAllergen and the datasets are available at https://services.healthtech.dtu.dk/services/NetAllergen-1.0/.
PanKmer: k-mer-based and reference-free pangenome analysis
Authors: Aylward Anthony J , Petrus Semar , Mamerto Allen , Hartwick Nolan T , Michael Todd P
Published: October 2023

Pangenomes are replacing single reference genomes as the definitive representation of DNA sequence within a species or clade. Pangenome analysis predominantly leverages graph-based methods that require computationally intensive multiple genome alignments, do not scale to highly complex eukaryotic genomes, limit their scope to identifying structural variants (SVs), or incur bias by relying on a reference genome. Here, we present PanKmer, a toolkit designed for reference-free analysis of pangenome datasets consisting of dozens to thousands of individual genomes. PanKmer decomposes a set of input genomes into a table of observed k-mers and their presence–absence values in each genome. These are stored in an efficient k-mer index data format that encodes SNPs, INDELs, and SVs. It also includes functions for downstream analysis of the k-mer index, such as calculating sequence similarity statistics between individuals at whole-genome or local scales. For example, k-mers can be “anchored” in any individual genome to quantify sequence variability or conservation at a specific locus. This facilitates workflows with various biological applications, e.g. identifying cases of hybridization between plant species. PanKmer provides researchers with a valuable and convenient means to explore the full scope of genetic variation in a population, without reference bias.

Availability and implementation

PanKmer is implemented as a Python package with components written in Rust, released under a BSD license. The source code is available from the Python Package Index (PyPI) at https://pypi.org/project/pankmer/ as well as Gitlab at https://gitlab.com/salk-tm/pankmer. Full documentation is available at https://salk-tm.gitlab.io/pankmer/.
ggkegg: analysis and visualization of KEGG data utilizing the grammar of graphics
Authors: Sato Noriaki , Uematsu Miho , Fujimoto Kosuke , Uematsu Satoshi , Imoto Seiya
Published: October 2023

The Kyoto Encyclopedia of Genes and Genomes (KEGG) database serves as a valuable systems biology resource and is widely utilized in diverse research fields. However, existing software does not allow flexible visualization and network analyses of the vast and complex KEGG data. We developed ggkegg, an R package that integrates KEGG information with ggplot2 and ggraph. ggkegg enables enhanced visualization and network analyses of KEGG data. We demonstrate the utility of the package by providing examples of its application in single-cell, bulk transcriptome, and microbiome analyses. ggkegg may empower researchers to analyze complex biological networks and present their results effectively.

Availability and implementation

The package and user documentation are available at: https://github.com/noriakis/ggkegg.
CAAStools: a toolbox to identify and test Convergent Amino Acid Substitutions
Authors: Barteri Fabio , Valenzuela Alejandro , Farré Xavier , de Juan David , Muntané Gerard , Esteve-Altava Borja , Navarro Arcadi
Published: October 2023

Motivation

Coincidence of Convergent Amino Acid Substitutions (CAAS) with phenotypic convergences allow pinpointing genes and even individual mutations that are likely to be associated with trait variation within their phylogenetic context. Such findings can provide useful insights into the genetic architecture of complex phenotypes.

Results

Here we introduce CAAStools, a set of bioinformatics tools to identify and validate CAAS in orthologous protein alignments for predefined groups of species representing the phenotypic values targeted by the user.

Availability and implementation

CAAStools source code is available at http://github.com/linudz/caastools, along with documentation and examples.
scHiCDiff: detecting differential chromatin interactions in single-cell Hi-C data
Authors: Liu Huiling , Ma Wenxiu
Published: October 2023

Here, we presented the scHiCDiff software tool that provides both nonparametric tests and parametirc models to detect differential chromatin interactions (DCIs) from single-cell Hi-C data. We thoroughly evaluated the scHiCDiff methods on both simulated and real data. Our results demonstrated that scHiCDiff, especially the zero-inflated negative binomial model option, can effectively detect reliable and consistent single-cell DCIs between two conditions, thereby facilitating the study of cell type-specific variations of chromatin structures at the single-cell level.

Availability and implementation

scHiCDiff is implemented in R and freely available at GitHub (https://github.com/wmalab/scHiCDiff).
PC_ali: a tool for improved multiple alignments and evolutionary inference based on a hybrid protein sequence and structure similarity score
Authors: Bastolla Ugo , Abia David , Piette Oscar
Published: October 2023

Motivation

Evolutionary inference depends crucially on the quality of multiple sequence alignments (MSA), which is problematic for distantly related proteins. Since protein structure is more conserved than sequence, it seems natural to use structure alignments for distant homologs. However, structure alignments may not be suitable for inferring evolutionary relationships.

Results

Here we examined four protein similarity measures that depend on sequence and structure (fraction of aligned residues, sequence identity, fraction of superimposed residues, and contact overlap), finding that they are intimately correlated but none of them provides a complete and unbiased picture of conservation in proteins. Therefore, we propose the new hybrid protein sequence and structure similarity score PC_sim based on their main principal component. The corresponding divergence measure PC_div shows the strongest correlation with divergences obtained from individual similarities, suggesting that it infers accurate evolutionary divergences. We developed the program PC_ali that constructs protein MSAs either de novo or modifying an input MSA, using a similarity matrix based on PC_sim. The program constructs a starting MSA based on the maximal cliques of the graph of these PAs and it refines it through progressive alignments along the tree reconstructed with PC_div. Compared with eight state-of-the-art multiple structure or sequence alignment tools, PC_ali achieves higher or equal aligned fraction and structural scores, sequence identity higher than structure aligners although lower than sequence aligners, highest score PC_sim, and highest similarity with the MSAs produced by other tools and with the reference MSA Balibase.

Availability and implementation

https://github.com/ugobas/PC_ali.