bluuebunny/crossref_metadata_2025 huggingface dataset:
Holistic scan optimization of nacelle-mounted lidars for inflow and wake characterization at the RAAW and AWAKEN field campaigns
Authors: Letizia Stefano , Bodini Nicola , Brugger Peter , Scholbrock Andrew , Hamilton Nicholas , Porté-Agel Fernando , Doubrawa Paula , Moriarty Patrick
Published: May 2023

In this article, we provide a methodological framework for designing the scanning strategies of nacelle-mounted scanning lidars for wind energy field experiments, and apply it at two major experimental field campaigns. For the Rotor Aerodynamics, Aeroelastics, and Wake project (RAAW), we leverage two scanning lidars on one turbine to characterize the incoming turbulence and the turbine wake. For the American WAKE experimeNt (AWAKEN), we use four scanning lidars on top of four turbines in a large wind power plant to investigate both individual wakes and wind-plant-scale flow features.
Stochastic wind farm flow generation using a reduced order model of LES
Authors: Andersen S. J. , Murcia Leon J. P.
Published: May 2023

Large eddy simulations are computationally expensive, which typically limits the simulation time and hence the statistics useful for validation. Here, a reduced order model with a stochastic engine is used to generate stochastic inflow to 48 wind turbines in the Lillgrund wind farm. The stochastic flow realization captures the power production and more importantly the correct cross-correlations in power and blade root flapwise bending moments over the large spatiotemporal region, which the wind farm covers. The analysis show how the cross-correlation increase further into the wind farm, where the highly turbulent flow becomes increasingly self-organized and how the dynamic interaction across the entire wind farm is captured by the first eight modes. Overall, the reduced order model captures the correct dynamics at a fraction of the computational cost, effectively generalizing the LES results beyond a relatively short simulation period.
Implications of complex terrain topography on the performance of a real wind farm
Authors: Bernardoni Federico , Guzman Miguel , Leonardi Stefano
Published: May 2023

Terrain topography affects the atmospheric boundary layer over a vertical region where wind turbines are usually located. It is commonly believed that placing wind turbines on the top of a ridge is beneficial because of the more energetic flow impinging on the turbines. However, the presence of topography with even modest altitude upstream of the wind farm may generate turbulent structures that significantly increase fluctuations in blade loads and power production.
Application of Green’s function in frequency solution for wind turbine blade modelled as box beam
Authors: Wang Jian , Chang Lin , Liu Tingrui
Published: May 2023

In order to study the vibration of composite wind turbine blades, a Green’s function method for frequency calculation is proposed. Based on the variational asymptotic method and Hamilton principle, the mechanical model of wind turbine blade, modelled as box beam with composite laminated structure, is established by using circumferential asymmetric stiffness design. The Green function method is used to analyze the frequency of wind turbine blades from the aspect of ply angle, and the numerical examples are compared with other calculation methods. The results show that the Green function method has good accuracy.
Research on algorithms of system vibration in yaw process of large wind turbine
Authors: Wang Zhiyuan , Wang Jian , Zhao Kang , Ji Zhongwei , Liu Tingrui
Published: May 2023

Aiming at the problem of system vibration during yawing of large wind turbines, the mathematical model is obtained by simulating the structure model of the yawing system, which is then represented by a general free vibration equation. The system vibration equation is modeled and simulated by MATLAB/Simulink. The model is controlled by PID, Fuzzy PID and Optimal Fuzzy PID intelligent algorithm, and the control result is obtained. By comparing the control results between different algorithms, it can be shown that although the PID algorithm and the Fuzzy PID algorithm can obviously and effectively control the vibration model of the yaw system, and the control effect of the Fuzzy PID algorithm is better than that of the PID algorithm, the PID parameters obtained by the “trial and compact method” are not the optimal parameters, which will affect the control effect of the Fuzzy PID. The Optimal Fuzzy PID algorithm can automatically optimize by MATLAB program to obtain the optimal PID parameters and achieve the optimal control effect.
Research on Online Diagnosis of Ship Main Engine with Unbalanced Sample
Authors: Wang Longde , Cao Hui , Wei Lai
Published: May 2023

The traditional ship main engine fault diagnosis model is difficult to update in real time. In addition, the main engine also has the problem of more monitoring parameters and less fault samples. In order to eliminate the influence of the above problems, improve the diagnostic accuracy. Firstly, in order to solve the problem that the traditional diagnosis model is difficult to update online in real time, Online Sequence Extreme Learning Machine is adopted as the diagnosis model, which can update the model directly online by using real-time samples. Then, for the problem that the sample set collected in the online update process is much smaller than the normal sample set, BorderlineSMOTE is used to generate fault samples to balance the sample set, and feature extraction and dimension reduction are carried out in combination with KPCA to further improve the training speed and diagnostic accuracy of the model. Taking the main engine fuel system as an example, the experimental results show that the proposed algorithm has high diagnostic accuracy and good stability, and is suitable for the research of ship main engine fault diagnosis.
Research on the Classification of Inherent Risks of Cranes Based on Interval Laminar Analysis Method-Index Method
Authors: Qi Zuoqiu , Li Mo , Zhao Xiaobing , Li Ronghua , Jiang Lili
Published: May 2023

In order to ensure the safe operation of cranes, from the perspective of the definition of inherent risk, the evaluation index of inherent risk of cranes was established. The interval hierarchy analysis method with better fuzziness was used to determine the index weights, determine the index scores of different levels, and use the integrated index method to establish a grading model, which was divided into four inherent risk levels according to the risk critical value. Application of the model to two cranes for example analysis, the results show that the model has good accuracy. The model provided a more scientific method for grading the inherent risk of cranes, which in turn provided a method of reference for grading the inherent risk of other types of special equipment.
Research on Design Principle and Process Design of Printed Circuit Board Type Overcurrent Protection Device for Chang’e-4 Popular Science Load Cable
Authors: Yang Qingjun , Hu Wenting , Cao Chenlei , Zhang Jin , Hu Jiujiu , Qi Fuqiang
Published: May 2023

The science popularization load of chang’e-4 is a high-density pressure resistant container with a diameter of 173 mm, a height of 198 mm and a weight of only 2.608 kg. It is loaded with cotton, rape, potato, Arabidopsis, yeast and Drosophila. With the successful landing of chang’e-4, this load has entered the growth and development mode of biological lunar surface. The data interface unit (DIU) of the lander provides the primary bus for the science popularization load system of Chang’e 4. The data interface unit provides no overcurrent protection measures for the power supply output. The science popularization load is provided with the command power supply by the lander system unit (SMU). The current limiting resistance of the power supply output is small, and there is moisture inside the science popularization load. In order to cope with the short circuit of the power supply bus and the command bus caused by the unexpected short circuit of the science popularization load power supply connector, In order to ensure the normal operation of popular science load equipment, the overcurrent protection design is considered on the power supply cable of popular science load.
Simulation Study of The Jerk System Based on Multisim
Authors: Lv Ensheng
Published: May 2023

Make an equivalent transformation of the equations of state for a class of Jerk systems, its chaotic dynamics behavior was analyzed. According to the equation of state, the schematic diagram of the chaotic circuit of the Jerk system was designed, and the Jerk circuit was simulated and experimented with Multisim software, and the corresponding two-dimensional phase diagram and time domain waveform diagram appeared, which explained the feasibility of simulating the chaotic circuit with Multisim, and was an effective experimental tool for studying and exploring the chaotic circuit.
A Robust Correlation Filtering Tracker Based on Joint Reliability Evaluation of Target Position Changes
Authors: Han Chao , Li Yixuan , Liu Qingyi , Pang Gang , Ma Xuechun , Fu Yingxia , Bai Peirui
Published: May 2023

Visual tracking is an important branch in computer vision. In complex scenarios, there exist various interference factors, e.g. background clutter, similar objects etc., making robust tracking based on correlation filter algorithm still a challenging task. In this paper, a correlation filter algorithm based on a novel adaptive multi-cue fusion strategy was proposed. First, a unified response map evaluation strategy was presented to assess the tracking reliability by combing the average peak correlation energy and the response peak historical information. Second, according to the cue reliability, an adaptive multi-cue fusion strategy was proposed to adaptively fuse two tracking cues, correlation filter and color histogram. The experimental results on OTB-2013 and UAV123 demonstrated that the proposed algorithm achieved competitive performance to the state-of the-art trackers.
Investigation and Analysis on the Present Situation of Rural Residential Buildings and Environment in Northeast China
Authors: Yu Liang , Huang Pengcheng
Published: May 2023

In order to realize the overall goal of energy saving and emission reduction in rural residential buildings and rural energy fields under the double-carbon goal and to promote the process of rural revitalization strategy, this paper analyzes the basic situation and existing problems of rural residential buildings, energy and other aspects by investigating and studying the basic situation of rural areas in Northeast China. The results show that the current rural residential buildings in Northeast China have been built for a long time, and the use of different rooms in the buildings is quite different, which greatly affects the indoor thermal environment and energy consumption under different heating forms. Rural heating equipment is more traditional, the utilization rate of clean energy is low, and there are some problems in the heating process, such as smoke pollution and uneven indoor temperature. The process of agricultural straw resource utilization is slow, and the problem of straw open burning is severe. Through the analysis and summary of the above problems, it will lay the foundation for the subsequent solution and improvement of rural residential buildings and energy problems in Northeast China.
Time-space consistency strategy for live-virtual-constructive (LVC) integrated simulation environment
Authors: Gao Yang , Deng Xiangyang , Zhang Yuanyuan , Zhou Xiaoguang
Published: May 2023

Constructing a unified Live-Virtual-Constructive (LVC) integrated simulation environment has always been a major goal in the modeling and simulation (M&S) field, and ensuring the time-space consistency is the foundation of its construction. That is, the inconsistency of time and space expression between integrated subsystems must be solved to achieve accurate and effective information interaction. To this end, this paper analyzes the specific causes of time-space inconsistency of LVC system, and gives the overall solution and the corresponding strategies or algorithms involved, including clock synchronization strategy, space coordinate conversion algorithm, time description conversion algorithm, dead reckoning (DR) algorithm and event causality control method. The relevant research has been verified in the integrated simulation system of missile attacking surface targets, and can provide technical support for the construction of large-scale LVC system.
A multi-state target recognition method based on multi-classifier fusion
Authors: Wang Dan , Hong Liang , Zhang Ce , Xiao Yong , Lin Ye
Published: May 2023

A multi-classifier target recognition algorithm based on fuzzy pattern recognition and fuzzy comprehensive evaluation theory is proposed, where the base classifiers are deployed as fuzzy pattern recognition classifiers, and the secondary classifiers are based on fuzzy comprehensive evaluation theory. On the basis of time-frequency domain analysis of target signals, fuzzy theories such as fuzzy pattern recognition, decision-making and comprehensive evaluation are synthetically applied to carry out first-level evaluation, where the extracted feature parameters are used as the input of target base classifiers. With the evaluation results as the input of second-level evaluation, target state recognition is performed on the multi-state human targets behind the walls in the ultra-wideband radar sensor network based on fuzzy evaluation. The results show that the recognition can efficiently discern the Multi-status human being behind the wall.
Design of Dual-Polarized Aperture-Coupled Microstrip Antenna with High Isolation at 28GHz
Authors: Yu Hailong
Published: May 2023

In this paper, a dual-polarized antenna with high isolation working at millimeter wave(mmW) frequency band is attempted. The proposed antenna can provide two orthogonal ports fed by only one square radiation patch with more than 30 dB isolation. In addition, the antenna can obtain a peal gain level of around 8dB for two ports. A more simple structure, which consists of two substrates and one foam layer rather than traditional two substrates, a cover plate and two foam layers, makes it more suitable for arrays form and easier for fabrication.
Regional Allocation Design and Efficiency Improvement of Rural Water Conservancy Project in China
Authors: Liu Yaqiong , Zhou Zhi , Huang Ying
Published: May 2023

Different development levels and speeds in different regions in China leads to the great difference in the allocation of rural water conservancy projects and the inefficiency. In order to improve the services function and configuration efficiency of rural China water conservancy infrastructure from water engineering, water supply engineering, reservoir engineering, the work chose the Chinese provincial panel data from 2017 to construct input-output indicator evaluation system with super-efficiency DEA. Then we designed the rural area of configuration of water conservancy projects for comparative analysis and China’s current rural water conservancy project region configuration system of geographical network coverage. Finally, based on the configuration in the grid lines, the method was proposed for efficiency. In order to analyze the regional difference in input-output efficiency of rural water conservancy construction, the panel data of 2017 was selected to establish the input-output indicator system of management efficiency. The results of super efficiency DEA show the general situation of input-output efficiency of rural water conservancy construction in China is not good, while there are some differences among input-output efficiency of rural water conservancy construction in East, West, Middle of China. Besides, Qinghai, Beijing, Hainan and Tibet are located in the last four. Finally, the four regions are all relatively effective with less than 100% super efficiency value, and four regions has redundant input in hydropower investment.
Dynamic Simulation Research of Flexible Airbag Ejection System Based on Corpuscular Method
Authors: Yan Song , Jiang Yi , Wen Xianghua , Zeng Peigao , Su Zhengyu
Published: May 2023

In order to reduce the weight of the missile launch system and reduce the cost of missile launch, a flexible airbag ejection system is studied to realize the work on the missile. The working mechanism and ejection performance of the flexible airbag ejection system are studied through numerical calculation. The results show that the ejection performance of the flexible airbag ejection system is related to factors such as the type and temperature of the ejection medium. In the study of the ejection medium, it is found that: the smaller the molar mass of the ejection medium and the higher the temperature, the better the ejection performance of the flexible airbag ejection system. The research results can provide an important reference for the design and optimization of the flexible airbag ejection system.
Dynamics model and numerical simulation of single stage water rocket
Authors: Ding Shaozhe , Liu Longbin , Zhang Shifeng
Published: May 2023

The initial launch parameters of a water rocket have a significant impact on its speed, altitude and other flight performance. The dynamic model describing the mass, velocity, nozzle velocity and internal pressure of water rocket was established by the force analysis of its ascending stage. Numerical simulation was carried out on the movement process of the water rocket. The changes of the internal pressure and thrust of the rocket body, and the speed and height law of the rocket in the flight process under the conditions of the same initial internal pressure and different initial loading propellant liquid were studied respectively. The results show that, under the designed conditions, the change law of the thrust force is similar to the variation of the internal air pressure in the ascending stage, and the internal air pressure decreases to 45%~57% of the initial value at last. Setting the volume of the initial loaded liquid to 0.43 helps to increase the boost duration and improve the utilization of the initial pressure, in which case, the maximum velocity of the launch rocket is not affected, but will lead to a decrease in thrust size.The above results provide important technical support for the optimal design of single-stage or multistage water rocket, and have strong guiding significance for carrying out water rocket flight test.
Cyberinfrastructure for sustainability sciences
Authors: Song Carol X , Merwade Venkatesh , Wang Shaowen , Witt Michael , Kumar Vipin , Irwin Elena , Zhao Lan , Walton Amy
Published: May 2023

Meeting the United Nation’ Sustainable Development Goals (SDGs) calls for an integrative scientific approach, combining expertise, data, models and tools across many disciplines towards addressing sustainability challenges at various spatial and temporal scales. This holistic approach, while necessary, exacerbates the big data and computational challenges already faced by researchers. Many challenges in sustainability research can be tackled by harnessing the power of advanced cyberinfrastructure (CI). The objective of this paper is to highlight the key components and technologies of CI necessary for meeting the data and computational needs of the SDG research community. An overview of the CI ecosystem in the United States is provided with a specific focus on the investments made by academic institutions, government agencies and industry at national, regional, and local levels. Despite these investments, this paper identifies barriers to the adoption of CI in sustainability research that include, but are not limited to access to support structures; recruitment, retention and nurturing of an agile workforce; and lack of local infrastructure. Relevant CI components such as data, software, computational resources, and human-centered advances are discussed to explore how to resolve the barriers. The paper highlights multiple challenges in pursuing SDGs based on the outcomes of several expert meetings. These include multi-scale integration of data and domain-specific models, availability and usability of data, uncertainty quantification, mismatch between spatiotemporal scales at which decisions are made and the information generated from scientific analysis, and scientific reproducibility. We discuss ongoing and future research for bridging CI and SDGs to address these challenges.
Antibacterial activity of silver nanoparticles created by one step nanosecond Nd: YAG laser ablation in water
Authors: Hasan Susan , Khashan Khawla S , Hadi Aseel A
Published: May 2023

The pulsed laser ablation in liquid (PLAL) technique was used to successfully synthesise silver nanoparticles (Ag NPs). With the goal of controlling their size, a laser wavelength of 1064 nm was focused on the Ag bulk target immersed in distilled water in a glass vessel with different laser fluences. The effect of laser fluence, and thus Ag NPs concentration on the bacterial pathogenic was investigated. While the Fourier-transform infrared spectroscopy (FTIR) and x-ray diffraction (XRD) patterns confirm the presence of Ag NPs, UV–vis spectrophotometry revealed a significant absorption peak at around 405 nm, which is attributed to the obtained Ag NPs’ characteristic surface plasmon resonance (SPR) peak. The SPR peak shifted towards a shorter wavelength as the laser fluence was increased, indicating that the Ag NPs have reduced in size. The transmission electron microscopy and size distribution images of Ag NPs clearly showed the effects of laser fluence on size reduction of Ag NPs. Bacteria activity was effectively inhibited by the Ag NPs which are found to be more effective against Gram-negative (Escherichia coli) than Gram-positive strains (Streptococcus aureus). PLAL has proven to be an effective method for controlling the size of NPs, which can be used in a variety of applications.
Determination of wear resistance of nickel-carbide alloy coating by atmospheric plasma spray technique on 30MnB5 alloy steel used in cultivator blades
Authors: Dilay Yusuf
Published: May 2023

The wear that occurs during tillage in agricultural machinery shortens the material’s life and increases costs. This study investigated the microstructure and morphology of cultivator blades coated with atmospheric plasma spray (APS) process and tested under real field conditions using OM, SEM, EDX, and XRD techniques. Abrasion tests were conducted in an area of 110 hectares and under two different soil moisture conditions. Material properties were investigated using hardness and surface roughness tests. The coating process was successful both mechanically and metallurgically by applying Ni-WC ceramic-metal (cermet) powder on the surface of 30MnB5 steel substrate with APS. The oxide and carbide structures detected on the coating surface by XRD studies resulted in a 1.5 times higher coating hardness. Due to the hard carbide phases in the coating matrix, the grooves on the wear surfaces were shallow and narrow compared to the substrate sample. The surface roughness values of the coated sample were approximately two times higher than the substrate sample. Due to the microstructure and high hardness, the coated specimen experienced three times less abrasion in both humidity conditions. The APS method can be successfully applied to the machined parts of tillage machines. In the near future, the cost of agricultural production can be reduced, and the environment can benefit from this method. In conclusion, this study presents a feasible approach to improving the wear resistance of Ni-WC ceramic-metal alloy by plasma spray coating under real field conditions.
Ag-doped CrN coating towards exhibiting excellent tribological and electrical properties under current-carrying friction
Authors: Hao Wu , Yanqiu Xia , Zhengfeng Cao , Lining Wu
Published: May 2023

In order to obtain sliding electrical contact materials with good conductivity and wear resistance, a series of silver doped chromium nitride (CrN-Ag) coatings were prepared by magnetron sputtering. The hardness, elastic modulus, chemical composition and surface morphology of the prepared coatings were characterized in detail. The tribological properties and conductivities of the prepared CrN-Ag coatings were investigated in detail at low and high current densities. The worn surfaces after friction test were also investigated to explore the lubrication mechanisms. The results show that the addition of Ag element could regulate the hardness, elastic modulus, chemical composition and surface morphology of the coatings. The CrN-Ag coating with 23 wt% Ag content exhibited the best conductive and tribological properties under low and high current densities. The analysis of friction surface shows that the conductivity and wear resistance of different coatings were mainly related to the Ag content of coatings.
Ammonium phosphotungstate nanoparticle/ultrathin g-C3N4 composite photocatalysts with Z-scheme heterojunctions: preparation and application to organic contaminant degradation
Authors: Li Pengxi , Liu Zhonghong , Tu Sheng , Jiang Wenming , Yang Jingjing
Published: May 2023

Owing to their advantageous physical, chemical, electronic, and optical properties, two-dimensional (2D) materials are widely used as highly active visible-light photocatalysts. In this study, 3D/2D composite photocatalysts were prepared from ammonium phosphotungstate nanoparticles and 2D ultrathin graphitic carbon nitride by an impregnation method and were found to efficiently promote the photodegradation of rhodamine B and tetracycline in water under visible light irradiation. Photocatalytic degradation was maximum at a PW12NH4 loading of 20 wt% (UCN20), with photodegradation efficiencies of 93.40% and 69.6% for RhB and TC, respectively. The photocatalytic degradation rate using UCN20 was 5.8-fold higher for RhB and 2.2-fold higher for TC compared to those with UCN. This high performance is ascribed to the large specific surface areas and pore volumes of the composites and the reduced probability of photogenerated carrier recombination therein. The related degradation mechanism is believed to involve a Z-scheme charge transfer mode, which enhances the redox capability of composite photocatalysts and renders them suitable for the visible light-driven remediation of wastewater containing organic contaminants.
Quantum dots: an overview of synthesis, properties, and applications
Authors: Agarwal Kushagra , Rai Himanshu , Mondal Sandip
Published: May 2023

Quantum dots (QDs) have sparked great interest due to their unique electronic, optical, and structural properties. In this review, we provide a critical analysis of the latest advances in the synthesis, properties, and applications of QDs. We discuss synthesis techniques, including colloidal and hydrothermal synthesis, and highlight how the underlying principles of these techniques affect the resulting properties of QDs. We then delve into the wide range of applications of QDs, from QDs based color conversion, light-emitting diodes and biomedicine to quantum-based cryptography and spintronics. Finally, we identify the current challenges and future prospects for quantum dot research. By reading this review, readers will gain a deeper understanding of the current state-of-the-art in QDs research and the potential for future development.
Preprint Highlight: mRNA Location and Translation Rate Determine Protein Targeting to Dual Destinations
Authors: Mantegazza Adriana R.
Published: May 2023

NET1 is a guanine nucleotide exchange factor for RhoA GTPase that plays different roles in the nucleus and cytoplasm. While perinuclear and peripheral mRNA translation sites have been identified, the mechanisms of spatial translation regulation and impacts on protein function are not generally understood. Here, the authors use genetic tools to manipulate NET1 mRNA targeting sequences, as well as proximity ligation, mass spectrometry, and imaging. They show that mRNA localization, translation rate, and the order of appearance of targeting domains during translation determine the extent of protein synthesis in each location, promoting site-specific NET1 function. This novel regulation of protein targeting by RNA translation rate and location uncovers the potential to engineer mRNA localization to optimize protein function and will likely impact research on cell biology, immunology, and beyond.

This preprint has been assigned the following badges: New Hypothesis, New Methods, Open Software, Cross-Validation.

Read the preprint on bioRxiv ( Gasparski et al., 2023 ): https://doi.org/10.1101/2023.04.24.538105 .
Preprint Highlight: Contractile ring mechanosensation and its anillin-dependent tuning during early embryogenesis
Authors: Landino Jennifer
Published: May 2023

Dividing cells assemble and constrict a contractile ring made up of actin and myosin anchored to the cell cortex. How the contractile ring senses the mechanics of the cell cortex is not known. With asymmetric ring closure in C. elegans as a model, the authors used novel 4D imaging and image segmentation methods to carefully track ring closure over time. They found that ring-directed cortical flow underlies mechanosensation and supports a positive feedback loop between ring closure, cortical flow, and myosin accumulation. These findings suggest that differences in cell cortex stiffness may determine the orientation and type of cell division–i.e., asymmetric vs. symmetric ring closure. As tissue morphogenesis often relies on specifically oriented cell divisions, defining mechanisms of ring closure is essential for understanding multicellular development.

This preprint has been assigned the following badges: New Methods, New Hypothesis.

Read the preprint on bioRxiv ( Hsu et al., 2023 ): https://doi.org/10.1101/2022.09.09.506560 .
Phen2Disease: a phenotype-driven model for disease and gene prioritization by bidirectional maximum matching semantic similarities
Authors: Zhai Weiqi , Huang Xiaodi , Shen Nan , Zhu Shanfeng
Published: May 2023

Human Phenotype Ontology (HPO)-based approaches have gained popularity in recent times as a tool for genomic diagnostics of rare diseases. However, these approaches do not make full use of the available information on disease and patient phenotypes. We present a new method called Phen2Disease, which utilizes the bidirectional maximum matching semantic similarity between two phenotype sets of patients and diseases to prioritize diseases and genes. Our comprehensive experiments have been conducted on six real data cohorts with 2051 cases (Cohort 1, n = 384; Cohort 2, n = 281; Cohort 3, n = 185; Cohort 4, n = 784; Cohort 5, n = 208; and Cohort 6, n = 209) and two simulated data cohorts with 1000 cases. The results of the experiments showed that Phen2Disease outperforms the three state-of-the-art methods when only phenotype information and HPO knowledge base are used, particularly in cohorts with fewer average numbers of HPO terms. We also observed that patients with higher information content scores have more specific information, leading to more accurate predictions. Moreover, Phen2Disease provides high interpretability with ranked diseases and patient HPO terms presented. Our method provides a novel approach to utilizing phenotype data for genomic diagnostics of rare diseases, with potential for clinical impact. Phen2Disease is freely available on GitHub at https://github.com/ZhuLab-Fudan/Phen2Disease.
The ACPYPE web server for small-molecule MD topology generation
Authors: Kagami Luciano , Wilter Alan , Diaz Adrian , Vranken Wim
Published: May 2023

Motivation

The generation of parameter files for molecular dynamics (MD) simulations of small molecules that are suitable for force fields commonly applied to proteins and nucleic acids is often challenging. The ACPYPE software and website aid the generation of such parameter files.

Results

ACPYPE uses OpenBabel and ANTECHAMBER to generate MD input files in Gromacs, AMBER, CHARMM, and CNS formats. It can now take a SMILES string as input, in addition to the original PDB or mol2 coordinate files, with GAFF2 support and GLYCAM force field conversion added. It can be installed locally via Anaconda, PyPI, and Docker distributions, while the web server at https://bio2byte.be/acpype/ was updated with an API, and provides visualization of results for uploaded molecules as well as a pre-generated set of 3738 drug molecules.

Availability and implementation

The web application is freely available at https://www.bio2byte.be/acpype/ and the open-source code can be found at https://github.com/alanwilter/acpype.
Gangs and the Gig Economy: Triads, Precarity and Illicit Work in Hong Kong
Authors: Fraser Alistair , Joe-Laidler Karen
Published: May 2023

Paid employment in the criminal economy is, in many ways, the essence of precarious labour yet to date criminological work on the so-called ‘gig economy’ is scarce. Here we apply emergent sociological literature on ‘post-Fordist’ working cultures to precarious youth employment in Hong Kong, arguing: (1) recent reorganizations of labour markets towards flexible entrepreneurship are mirrored in the illicit economy; (2) a shift in structural features of triad gangs has led to a parallel form of ‘network sociality’; and (3) triad-affiliated youth remained rooted in place-based ‘communities of practice’ that form a point of difference from existing theory. In concluding, we reflect on the implications of these arguments for the study of illicit economies, triads and post-Fordist working cultures.
Cardiovascular complications in chronic kidney disease: a review from the European Renal and Cardiovascular Medicine Working Group of the European Renal Association
Authors: Zoccali Carmine , Mallamaci Francesca , Adamczak Marcin , de Oliveira Rodrigo Bueno , Massy Ziad A , Sarafidis Pantelis , Agarwal Rajiv , Mark Patrick B , Kotanko Peter , Ferro Charles J , Wanner Christoph , Burnier Michel , Vanholder Raymond , Wiecek Andrzej
Published: May 2023

Chronic kidney disease (CKD) is classified into five stages with kidney failure being the most severe stage (stage G5). CKD conveys a high risk for coronary artery disease, heart failure, arrhythmias, and sudden cardiac death. Cardiovascular complications are the most common causes of death in patients with kidney failure (stage G5) who are maintained on regular dialysis treatment. Because of the high death rate attributable to cardiovascular (CV) disease, most patients with progressive CKD die before reaching kidney failure. Classical risk factors implicated in CV disease are involved in the early stages of CKD. In intermediate and late stages, non-traditional risk factors, including iso-osmotic and non-osmotic sodium retention, volume expansion, anaemia, inflammation, malnutrition, sympathetic overactivity, mineral bone disorders, accumulation of a class of endogenous compounds called ‘uremic toxins’, and a variety of hormonal disorders are the main factors that accelerate the progression of CV disease in these patients. Arterial disease in CKD patients is characterized by an almost unique propensity to calcification and vascular stiffness. Left ventricular hypertrophy, a major risk factor for heart failure, occurs early in CKD and reaches a prevalence of 70–80% in patients with kidney failure. Recent clinical trials have shown the potential benefits of hypoxia-inducible factor prolyl hydroxylase inhibitors, especially as an oral agent in CKD patients. Likewise, the value of proactively administered intravenous iron for safely treating anaemia in dialysis patients has been shown. Sodium/glucose cotransporter-2 inhibitors are now fully emerged as a class of drugs that substantially reduces the risk for CV complications in patients who are already being treated with adequate doses of inhibitors of the renin-angiotensin system. Concerted efforts are being made by major scientific societies to advance basic and clinical research on CV disease in patients with CKD, a research area that remains insufficiently explored.
Dementia and electronic health record phenotypes: a scoping review of available phenotypes and opportunities for future research
Authors: Walling Anne M , Pevnick Joshua , Bennett Antonia V , Vydiswaran V G Vinod , Ritchie Christine S
Published: May 2023

Objective

We performed a scoping review of algorithms using electronic health record (EHR) data to identify patients with Alzheimer’s disease and related dementias (ADRD), to advance their use in research and clinical care.

Materials and Methods

Starting with a previous scoping review of EHR phenotypes, we performed a cumulative update (April 2020 through March 1, 2023) using Pubmed, PheKB, and expert review with exclusive focus on ADRD identification. We included algorithms using EHR data alone or in combination with non-EHR data and characterized whether they identified patients at high risk of or with a current diagnosis of ADRD.

Results

For our cumulative focused update, we reviewed 271 titles meeting our search criteria, 49 abstracts, and 26 full text papers. We identified 8 articles from the original systematic review, 8 from our new search, and 4 recommended by an expert. We identified 20 papers describing 19 unique EHR phenotypes for ADRD: 7 algorithms identifying patients with diagnosed dementia and 12 algorithms identifying patients at high risk of dementia that prioritize sensitivity over specificity. Reference standards range from only using other EHR data to in-person cognitive screening.

Conclusion

A variety of EHR-based phenotypes are available for use in identifying populations with or at high-risk of developing ADRD. This review provides comparative detail to aid in choosing the best algorithm for research, clinical care, and population health projects based on the use case and available data. Future research may further improve the design and use of algorithms by considering EHR data provenance.
Efficient ways to combine data from broiler and layer chickens to account for sequential genomic selection
Authors: Hidalgo Jorge , Lourenco Daniela , Tsuruta Shogo , Bermann Matias , Breen Vivian , Herring William , Misztal Ignacy
Published: May 2023

In broiler breeding, superior individuals for growth become parents and are later evaluated for reproduction in an independent evaluation; however, ignoring broiler data can produce inaccurate and biased predictions. This research aimed to determine the most accurate, unbiased, and time-efficient approach for jointly evaluating reproductive and broiler traits. The data comprised a pedigree with 577K birds, 146K genotypes, phenotypes for three reproductive (egg production [EP], fertility [FE], hatch of fertile eggs [HF]; 9K each), and four broiler traits (body weight [BW], breast meat percent [BP], fat percent [FP], residual feed intake [RF]; up to 467K). Broiler data were added sequentially to assess the impact on the quality of predictions for reproductive traits. The baseline scenario (RE) included pedigrees, genotypes, and phenotypes for reproductive traits of selected animals; in RE2, we added their broiler phenotypes; in RE_BR, broiler phenotypes of nonselected animals, and in RE_BR_GE, their genotypes. We computed accuracy, bias, and dispersion of predictions for hens from the last two breeding cycles and their sires. We tested three core definitions for the algorithm of proven and young to find the most time-efficient approach: two random cores with 7K and 12K animals and one with 19K animals, containing parents and young animals. From RE to RE_BR_GE, changes in accuracy were null or minimal for EP (0.51 in hens, 0.59 in roosters) and HF (0.47 in hens, 0.49 in roosters); for FE in hens (roosters), it changed from 0.4 (0.49) to 0.47 (0.53). In hens (roosters), bias (additive SD units) decreased from 0.69 (0.7) to 0.04 (0.05) for EP, 1.48 (1.44) to 0.11 (0.03) for FE, and 1.06 (0.96) to 0.09 (0.02) for HF. Dispersion remained stable in hens (roosters) at ~0.93 (~1.03) for EP, and it improved from 0.57 (0.72) to 0.87 (1.0) for FE and from 0.8 (0.79) to 0.88 (0.87) for HF. Ignoring broiler data deteriorated the predictions’ quality. The impact was significant for the low heritability trait (0.02; FE); bias (up to 1.5) and dispersion (as low as 0.57) were farther from the ideal value, and accuracy losses were up to 17.5%. Accuracy was maintained in traits with moderate heritability (~0.3; EP and HF), and bias and dispersion were less substantial. Adding information from the broiler phase maximized accuracy and unbiased predictions. The most time-efficient approach is a random core with 7K animals in the algorithm for proven and young.
Annular rupture during transcatheter aortic valve replacement in a long-term corticosteroid user: a case report
Authors: Nishiori Hironobu , Matsuura Kaoru , Yakita Yasunori , Kanda Tomoyoshi , Kitahara Hideki , Yamashita Daichi , Kobayashi Yoshio , Matsumiya Goro
Published: May 2023

A 74-year-old woman with a history of interstitial pneumonia, who had been taking oral corticosteroids for the past 9 years, was diagnosed with severe aortic stenosis. The patient underwent transfemoral transcatheter aortic valve replacement (TAVR) with a balloon-expandable valve under local anesthesia. After deploying a 26-mm SAPIEN 3 valve with 1.5 ml less balloon inflation, transesophageal echocardiography revealed a hemorrhage in the aortic annulus. Intraoperative angiography revealed a small contrast leakage around the ascending aorta. Emergent surgical aortic valve replacement was performed successfully, with a tear at the non-left commissure closed using interrupted sutures. The patient was discharged on postoperative day 14 with no paravalvular leakage. Chronic corticosteroid use may be a risk factor for annular ruptures during TAVR. Careful balloon dilation may be necessary, especially when balloon-expandable valves are used in patients receiving long-term corticosteroids.
Metagenomic next-generation sequencing for the identification of infections caused by Gram-negative pathogens and the prediction of antimicrobial resistance
Authors: Xiao Yang-Hua , Luo Zhao-Xia , Wu Hong-Wen , Xu De-Rong , Zhao Rui
Published: May 2023

Objective

The aim of this study was to evaluate the efficacy of metagenomic next-generation sequencing (mNGS) for the identification of Gram-negative bacteria (GNB) infections and the prediction of antimicrobial resistance.

Methods

A retrospective analysis was conducted on 182 patients with diagnosis of GNB infections who underwent mNGS and conventional microbiological tests (CMTs).

Results

The detection rate of mNGS was 96.15%, higher than CMTs (45.05%) with a significant difference (χ 2 = 114.46, P < .01). The pathogen spectrum identified by mNGS was significantly wider than CMTs. Interestingly, the detection rate of mNGS was substantially higher than that of CMTs (70.33% vs 23.08%, P < .01) in patients with but not without antibiotic exposure. There was a significant positive correlation between mapped reads and pro-inflammatory cytokines (interleukin-6 and interleukin-8). However, mNGS failed to predict antimicrobial resistance in 5 of 12 patients compared to phenotype antimicrobial susceptibility testing results.

Conclusions

Metagenomic next-generation sequencing has a higher detection rate, a wider pathogen spectrum, and is less affected by prior antibiotic exposure than CMTs in identifying Gram-negative pathogens. The mapped reads may reflect a pro-inflammatory state in GNB-infected patients. Inferring actual resistance phenotypes from metagenomic data remains a great challenge.
Bulbar onset amyotrophic lateral sclerosis with more evident symptoms in the left hemibody: a case report
Authors: Chavan Manisha , Singh Ajay , Bathvar Pinank K , Mehta Sarang T , Qadree Abdul K , Dhakal Sandesh
Published: May 2023

Amyotrophic lateral sclerosis (ALS) is a progressive, degenerative neuromuscular condition. The procedure and difficulties involved in the clinical diagnosis of ALS have been the subject of numerous investigations. The understanding of the genetics and the epigenetics of the disease is still at infancy with several missing links. We present a case report of a 73-year-old woman suffering from bulbar onset ALS with a 4-month history of progressive dysphagia and dyspnea. She displayed tongue fasciculations and muscle atrophy. The bilateral palmomental reflexes, snout reflex, Hoffman, Babinski, diminished gag reflex, bilateral clonus and wild mood swings confirmed the neurodegenerative condition of the patient. The diagnosis of ALS can be challenging; therefore, the data presented may be useful to investigate its characteristics of the onset and to improve the understanding of the aspects of differentiation from other neurodegenerative disorders.
Pyroglutamic acidosis caused by the combination of two common medicines prescribed in everyday practice
Authors: Duncan A , McDermott H , Corcoran S , Devine C , Barry C
Published: May 2023

We present the case of a 71-year-old female treated for infective endocarditis with flucloxacillin and paracetamol. Her clinical course became complicated by a blood-gas demonstrating a raised anion gap metabolic acidosis. The patient was diagnosed with pyroglutamic metabolic acidosis. This is a rare interaction between high dose flucloxacillin and paracetamol, and is an important complication to recognize.
Winter range shifts and their associations with species traits are heterogeneous in eastern North American birds
Authors: Laughlin Andrew J , Pomara Lars Y
Published: May 2023

Many species’ distributions are shifting in response to climate change. Many distributional shifts are predictably poleward or higher in elevation, but heterogeneity in the rate and direction of shifts both within and between species appears to be common. We found high heterogeneity in the trajectory of winter range shifts for 65 species of birds across eastern North America and in the different traits and trait interactions associated with these shifts across the spatial scales we examined. We used data from the Christmas Bird Count to quantify the trajectory of winter latitudinal center of abundance range shifts over 4 decades (1980–2019) for 65 species of songbirds and woodpeckers in North America, both across eastern North America (ENA) as a whole and for the Atlantic (ATL) and Mississippi (MISS) flyways separately. We then used linear models and Akaike’s Information Criterion with small-sample size correction (AICc) model selection to test whether species traits could explain variation in range shifts or flyway discrepancies. Across ENA, most species showed northward latitudinal range shifts, but some showed no latitudinal shift while others shifted southwards. Amongst ATL and MISS, we documented both within- and between-species differences in the rate and direction of latitudinal shifts, complicating the results from across ENA. No single trait emerged as a dominant driver of range shift differences at the ENA and flyway scales. Migration strategy interacted with insectivory to explain variation at the largest spatial scale (ENA), whereas frugivory and mean winter latitude explained much of the variation in ATL and MISS, respectively. Exploring heterogeneity in range shifts within and between species, and in the associations between range shifts and life history traits, will help us better understand the mechanisms that mediate differing responses to environmental change and predict which species will be better able to adapt to those changes.
The Role of Federalism and the Centrality of State Governments for Labor Unions, Employment, and Organizing
Authors: Bucci Laura C
Published: May 2023

American states differ in their protection of workers, acceptance of organized labor, dominant industrial cultures, and regarding labor unions’ capacity and political power. In this article, I examine declining union membership in the states and analyze various laws that limit the political power of unions and assess the consequences of these developments. I also document and explain a recent resurgence of labor organizing, political resistance, and work stoppages. There is a seeming contradiction between a labor movement that is both declining as well as gaining strength. However, a common theme in each of these trends is the centrality of state governments and politics regarding labor policy and union influence.