bluuebunny/crossref_metadata_2025 huggingface dataset:
Simulation study on the impact of heat source intensity on the inhaled air quality of an innovative personalized air supply method
Authors: Ma Zewei
Published: July 2024

To improve the local microenvironment of the human body in industrial buildings with strong heat sources, this paper proposes a new personalized air supply method based on the attachment effect. The numerical simulation method is used to study the influence of heat source intensity on the inhaled air quality in this paper. Studies have shown that when the air supply speed is less than or equal to 0.5 m/s, the fresh air ratio decreases as the Gr number of the heat source increases. When the air supply speed is greater than or equal to 0.7 m/s, the fresh air ratio increases as the Gr number of the heat source increases.
Dynamic simulation of a simply supported beam subjected by multiple constant moving forces
Authors: Zhang Jun , Liang Chuan , Zhu Pengcheng
Published: July 2024

Dynamic simulation models, which are conducted with Simulink, are introduced to study behaviors of a simply supported beam under constant moving forces based on the vibration mechanics model established by Bernoulli-Euler beam theory. By utilizing the orthogonality of vibration, a set of decoupled forced vibration equations can be obtained, which can be constructed as a subsystem of the Simulink model. The generalized loads in each decoupled vibration equation are also separately formed into submodules to facilitate the extension of the action of a single moving load to multiple moving loads. Every partial and general simulation model in Matlab/Simulink are made and the simulation results indicate that dynamic responses are related to the distance between moving loads and beam span.
Model establishment and flow field simulation analysis of high torque screw motor in ultra-deep well
Authors: Yang Chengsong , Lin Tiejun , Zeng Xin , Zhu Zelin , Shen Ruiqi
Published: July 2024

To explore the distribution law of the flow field in the inner annular flow channel of the stator-rotor of the high-torque screw drill tool and determine the key performance parameters of the tool under different drilling fluid densities and flow rates, a physical model for fluid simulation was established with the 7/8 head screw motor as the research object to study the distribution law of the flow field and the output torque of the rotor at different flow rates and densities, and a comparative analysis was made with the actual test. The results show that the pressure of the internal flow channel is mainly concentrated at the entrance of the flow channel and the wall of the flow channel. The flow rate in the thick fluid domain is high, the flow rate in the thin fluid domain is low, and the flow rate in the thinnest area is about zero. The relationship between displacement pressure drop and output torque presents a positive correlation. When displacement increases, the output torque of the screw increases, and the relationship between displacement and torque presents a linear increase. The torque and displacement of fluid simulation under ideal conditions are larger than the actual test parameters. In the actual test, the drilling fluid temperature and experimental equipment factors affect the performance of the screw motor. In the process of fluid simulation, the setting of boundary conditions should refer to the real situation as much as possible to improve the accuracy of simulation results. The difference between fluid simulation and actual test parameter values is small and the trend is the same, so fluid simulation can guide practical application and reduce cost to a certain extent.
Strength analysis and structural improvement of the connection between rear shock absorber support and frame of a city bus based on Hypermesh
Authors: Li Xiaoying , Zhuang Shouji
Published: July 2024

In response to the phenomenon of cracking at the rivet holes of the plate connecting the rear shock absorber to the frame of the 6-meter leaf spring of the passenger bus, this article takes the rear shock absorber support and the frame as the research object. Firstly, CATIA software is used to model the object, and Hypermesh is used to divide the mesh to establish a fine element model. The Optistruct finite element solver is used to analyze the strength of the model, and the analysis results are imported into Hyperview 2019 for post-processing to analyze stress distribution and stress concentration. The simulation analysis results show that when a force of 6, 721 N is applied to the rear shock absorber support, the maximum stress value occurs at the rivet holes of the plate connecting the support to the frame, and the maximum equivalent stress value at this point is greater than the yield limit of the frame material, which is consistent with the crack location that occurs during actual vehicle operation. After adopting the strengthening scheme, the stress distribution of the frame is more uniform, greatly reducing stress concentration. The maximum stress value appears on the inner side of the right frame, and the maximum equivalent stress is less than the yield limit of the frame material, avoiding the crack phenomenon. The results indicate that this scheme can not only meet the performance requirements but also provide a reference for structural improvement and optimization design of the connection between the rear shock support and the frame.
Order reduction of special valve models based on pod method
Authors: Zuo Lu , Bai Keqiang , Zhu Yalan , Jiang Hesong , Gong Xuantao
Published: July 2024

The opening size of the disc-type special regulating valve (referred to as the special valve) can be used to regulate the fluid pressure and flow inside the cabin, and is an important equipment in the intake system of the high-altitude simulation test bench (referred to as the high-altitude bench). Due to the high dimensionality and complex solution of the special valve model, the calculation time is relatively long. In this paper, the Proper Orthogonal Decomposition (POD) model reduction method is applied to the mathematical model of the special valve, and the POD basis matrix is constructed through snapshots, thus obtaining a low-dimensional model and improving computational efficiency. The research results indicate that, while ensuring sufficient accuracy, this method can reduce the dimensionality of the special valve model, improve the computational speed of the simulator in calculating this case, and verify the effectiveness of the POD method.
Study on simulation method of propeller cavitation
Authors: Wang Ru
Published: July 2024

With the continuous improvement of EEDI requirements and high fuel prices, people have higher and higher requirements for the efficiency of merchant propellers, but the efficiency of propellers is limited by cavitation, so it is one of the difficult problems in engineering to quickly evaluate the cavitation performance of propellers. The cavitation performance of the propeller in a viscous uniform flow field is calculated and studied by using computational fluid dynamics commercial software, and the cavitation distribution on the blade surface of the DTMB 4381 propeller under specific working conditions is simulated to study the influence mechanism of cavitation performance. It provides an important guiding direction for the optimal design of propellers and the reduction of ship energy consumption.
Research on three-dimensional dynamic design and decision system of airport
Authors: Shen Peng , Zhang Yan
Published: July 2024

Due to the lack of elevation information, the traditional airport design system based on the AutoCAD 2D platform is often unable to make a comprehensive and objective analysis and judgment when the designer evaluates the advantages and disadvantages of the design scheme. Therefore, this paper focuses on the development of airport 3D dynamic design and decision systems based on the Cesium framework. Firstly, based on the 3D geographic information platform, a multi-type 3D digital map loading and display module will be developed to realize the combination of 3D geographic information and the airfield model. Then, according to the 3D model data and the characteristics of the platform development, the method of calculating the earth volume of clearance processing, the evaluation algorithm of airport clearance obstacle limit surface, the optimization analysis method of tower position, and the analysis method of navigation station and flight track visibility are constructed.
Multi-objective topology optimization simulation study based on motor
Authors: Li Qiding , Huang Zhengping , Li Ketian , Wang Xiying , Yu Cheng , Li Bing
Published: July 2024

OptiStruct software is applied for structural optimization of the motor structure to solve the problem of resonance in a specific operating frequency range and reduce the motor operating noise. Comparing the experimental and simulated modal frequencies, a modified multi-objective topology optimization model is proposed to ensure the validity of the model, and a new optimization function is constructed to optimize the multi-objective topology of the motor housing. The results show that the geometric reconfiguration of the motor housing concerning the optimized model force transmission path achieves the effectiveness of reducing resonance noise. The multi-objective topology optimization model provides a feasible way to solve the motor-specific frequency resonance and operation noise problems.
A novel tuning range search method for single soliton state micro-comb generation
Authors: Ma Xi , Zhao Yi , Zhao Weigang , Tan Qinggui
Published: July 2024

Mode-locked single-soliton state micro-comb (SSC) can be achieved in a miniaturized highly compact platform by pumping the micro-resonator with a single-frequency continuous wave laser. However, a significant challenge lies in effectively exploring the tuning range of pump power, spanning over hundreds of mW, as well as the detuning range and tuning speed in the range of hundreds of MHz and the order of MHz/s to GHz/s respectively. Here, we delve into a simulation model, considering thermal effects to ensure that the simulation accurately reflects the power drop and thermal detuning observed in the experimental process. Our simulation model, featuring precision scanning and iterative parameter demonstrations, has proven instrumental in accurately exploring the optimal tuning range for the existence of SSC to a few MHz. This provides a foundation for controlled and predictable SSC generation experiments.
Design of petal-shaped probe for pulse eddy current testing based on finite element simulation
Authors: Zhou Haiting , Zhu Chenxi , Hu Qin , Mu Yanchun
Published: July 2024

This paper employs finite element simulation techniques to devise an innovative array-type petal-shaped pulsed eddy current testing probe and investigates its distinctions related to conventional cylindrical probes. Within the simulation framework, a thorough comparative analysis of the detection capabilities of the two probe types is conducted, encompassing an examination of the eddy current regions formed, the impact of lift-off effects and sensitivity to circular corrosion defects. The simulation outcomes reveal that the probe designed in this study exhibits a more extensive detection range and superior detection performance in comparison to its counterparts. This observation holds significance for defect detection in coated materials and the refinement of pulsed eddy current testing probe designs.
Target threat assessment model based on PCA-BP neural network
Authors: Shang Jielin , Chen Tong , Dou Jie
Published: July 2024

In this paper, the air threat received in modern naval warfare is taken as the background, and based on the threat assessment index, PCA and BP neural networks are used to establish a target threat assessment model. Through simulation and analysis, the threat values of different incoming targets are derived, and the data results of this model and other models are compared. It is concluded that the results of this model are basically consistent with the original values, and the error is significantly smaller than that of the other models, which realizes the real-time dynamic detection of threatening targets, and provides a strong support for the subsequent combat program.
Performance of PSG in retrieving exoplanet parameters from JWST data simulated with several tools
Authors: Barbier H. , López E. , Mayorga D. , Cherres D.
Published: July 2024

Our research explores different methods of utilizing several known tools (petitRADTRANS, PandExo, and PSG) to simulate spectral data acquired by the James Webb Space Telescope (JWST). We specifically focus on how the choice of method affects the performance of the Planetary Spectrum Generator (PSG) in retrieving exoplanet parameters from such data. To investigate this, we consider the case of exoplanet TOI-1266 c being observed by JWST’s Near Infrared Spectrograph in the Bright Object Time Series mode. Our results show that differences between PSG and PandExo regarding their noise simulation and method of adjusting spectral resolution lead to significant differences in retrieval quality. When utilizing PandExo to simulate noise for non-binned down spectral data, we recommend ensuring that the resolution of the theoretical forward model spectrum input into PandExo closely matches the resolution of the output spectral data, within the same order of magnitude.
About the 3D virtualization of the Millikan oil drop experiment
Authors: Ronquillo Daniel
Published: July 2024

Robert Millikan’s experiment, conducted in 1909, aimed to measure the charge of the electron. This experiment holds immense significance in the fields of electricity and magnetism and is widely performed by physics and chemistry students worldwide. While there are simplified two-dimensional recreations of this experiment available, obtaining measurements that closely resemble reality through a three-dimensional recreation is not easily accessible. This article delves into the development process of this three-dimensional recreation, achieved through reverse engineering of the original experiment using the Unity video game engine. Additionally, it incorporates laboratory equipment, user manuals, and a student guide to ensure a comprehensive experience. By comparing the data obtained from the virtual recreation with that of the real experiment, it was observed that the precision of the virtual experiment resulted in a mere 7% error. Consequently, the virtual experiment can be used as a substitute for the real experiment when circumstances prevent its execution, without compromising the hands-on experience.
Sokoban percolation on the Bethe lattice
Authors: Bonomo Ofek Lauber , Shitrit Itamar , Reuveni Shlomi
Published: July 2024

‘With persistence, a drop of water hollows out the stone’ goes the ancient Greek proverb. Yet, canonical percolation models do not account for interactions between a moving tracer and its environment. Recently, we have introduced the Sokoban model, which differs from this convention by allowing a tracer to push single obstacles that block its path. To test how this newfound ability affects percolation, we hereby consider a Bethe lattice on which obstacles are scattered randomly and ask for the probability that the Sokoban percolates through this lattice, i.e. escapes to infinity. We present an exact solution to this problem and determine the escape probability as a function of obstacle density. Similar to regular percolation, we show that the escape probability undergoes a second-order phase transition. We exactly determine the critical obstacle density at which this transition occurs and show that it is higher than that of a tracer without obstacle-pushing abilities. Our findings assert that pushing facilitates percolation on the Bethe lattice, as intuitively expected. This result, however, sharply contrasts with our previous findings on the 2D square lattice, where the Sokoban cannot escape even at obstacle densities well below the regular percolation threshold. This indicates that the presence of a regular percolation transition does not guarantee a percolation transition for a pushy tracer. The stark contrast between the Bethe and 2D lattices also highlights the significant impact of network topology on the effects of obstacle pushing and underscores the necessity for a more comprehensive understanding of percolation phenomena in systems with tracer-media interactions.
Corrigendum to “Airfoil friction drag reduction based on grid-type and super-dense array plasma actuators”
Authors: FANG 方 Ziqi 子淇 , ZONG 宗 Haohua 豪华 , WU 吴 Yun 云 , LIANG 梁 Hua 华 , SU 苏 Zhi 志
Published: July 2024

Figure 4(b) of the paper [Plasma Sci. Technol.
26 (2024) 025503] has been corrected. This modification does not affect the result presented in the paper.
Regulating electronic structure of anionic oxygen by Ti4+ doping to stabilize layered Li-rich oxide cathodes for Li-ion batteries
Authors: Zhu Xinyu , Hao Luqi , Li Yongjian , Chen Lai , Huang Qing , Lu Yun , Li Ning , Su Yuefeng
Published: July 2024

Layered Li-rich oxide cathodes enable to activate lattice oxygen anions redox in the charge compensation process and provide superior high specific capacity over 250 mAh g−1 due to their unique configuration, and thus attracting great attentions as promising cathode candidates for Li-ion batteries. However, how to better stabilize the bulk lattice oxygen framework and surface structure, and slow down the release of oxygen, is still major bottleneck to develop high performance Li-rich materials. Transition metal ions with outer d0 electronic configuration have distortable configuration, which can accommodate the local structure and chemical environment of the material, and then improve structural stability. Herein this work, the d0 transition metal Ti4+ is used as doping element to improve the chemical and structural stability, capacity retention and lithium ion diffusion kinetics of Li-rich material. The role of Ti in the material modification is revealed through synchrotron-based soft x-ray absorption spectroscopy, XRD, XPS and electrochemical tests. The improvement in structural stability can be attributed to that Ti doping can adjust the hybridization of O2p and TM3d to regulate the local electronic structure of both bulk lattice oxygen and surface oxygen vacancies. It is hoped that this work should shed light on the development of high-performance cathode materials for Li-ion Batteries.
Agreement between the National Cancer Institute’s Diet History Questionnaire II and III in a preconception cohort
Authors: Julián-Serrano Sachelly , Koenig Martha R , Wang Tanran R , Wesselink Amelia K , Hatch Elizabeth , Wise Lauren A , Tucker Katherine L
Published: July 2024

Food frequency questionnaires require updating over time due to population changes in diet, posing analytical challenges in consistently measuring diet in prospective studies. We compared reliability and agreement between nutrients in versions of the National Cancer Institute’s web-based Diet History Questionnaire (DHQ, III vs II) in an ongoing North American preconception study. We invited 51 consecutively enrolled US female participants aged 21-45 years to complete both DHQ versions within a 2-week period in a randomized order. We compared 30 nutrients from both DHQ versions and calculated within-person reliability using intraclass correlation coefficients (ICCs). Bland–Altman plots and 95% limits of agreement (LOA) were generated to assess nutrient agreement between DHQ versions. We observed highest reliability in percent energy from carbohydrates and cholesterol (ICCs, 0.88; 95% IC, 0.80-0.93) and lowest for percent energy from protein and vitamin D (ICCs, 0.56; 95% IC, 0.34-0.72). At the group level, all nutrients had most observations within the LOA. Bland–Altman plots showed assessment differences between DHQs for protein, fat, monounsaturated fat, and vitamin D. The remaining nutrients showed good agreement and good to moderate reliability. Some nutrients may require adjustment and calibration analysis before using them interchangeably across DHQ versions.
Invited commentary: deep learning—methods to amplify epidemiologic data collection and analyses
Authors: Quistberg D Alex , Mooney Stephen J , Tasdizen Tolga , Arbelaez Pablo , Nguyen Quynh C
Published: July 2024

Deep learning is a subfield of artificial intelligence and machine learning, based mostly on neural networks and often combined with attention algorithms, that has been used to detect and identify objects in text, audio, images, and video. Serghiou and Rough (Am J Epidemiol. 2023;192(11):1904-1916) presented a primer for epidemiologists on deep learning models. These models provide substantial opportunities for epidemiologists to expand and amplify their research in both data collection and analyses by increasing the geographic reach of studies, including more research subjects, and working with large or high-dimensional data. The tools for implementing deep learning methods are not as straightforward or ubiquitous for epidemiologists as traditional regression methods found in standard statistical software, but there are exciting opportunities for interdisciplinary collaboration with deep learning experts, just as epidemiologists have with statisticians, health care providers, urban planners, and other professionals. Despite the novelty of these methods, epidemiologic principles of assessing bias, study design, interpretation, and others still apply when implementing deep learning methods or assessing the findings of studies that have used them.
Invited commentary: policies that support working parents and gender health equity—needed research and methodological challenges
Authors: Schnake-Mahl Alina , Jahn Jaquelyn
Published: July 2024

In a recent issue of the Journal, Platt et al (Am J Epidemiol. 2024;193(10):1362-1371) shed new light on the potential for supportive employment benefits, including family leave, flexible work hours, and employer-provided or subsidized childcare, to mitigate the risk of depression among full-time working mothers. The authors used a longitudinal study design and rigorous methods to carefully consider potential sources of bias, and, more broadly, their article underscores the importance of employment benefits as a social determinant of mental health for working mothers. In this commentary, we discuss some of the policy context surrounding employer benefits that support parenting, particularly around paid versus unpaid family leave laws and ordinances. We consider the ways in which the policy context affects larger structural inequities and the potential implications for internal and external validity.

This article is part of a Special Collection on Mental Health.
A survey of generative AI for de novo drug design: new frontiers in molecule and protein generation
Authors: Tang Xiangru , Dai Howard , Knight Elizabeth , Wu Fang , Li Yunyang , Li Tianxiao , Gerstein Mark
Published: July 2024

Artificial intelligence (AI)-driven methods can vastly improve the historically costly drug design process, with various generative models already in widespread use. Generative models for de novo drug design, in particular, focus on the creation of novel biological compounds entirely from scratch, representing a promising future direction. Rapid development in the field, combined with the inherent complexity of the drug design process, creates a difficult landscape for new researchers to enter. In this survey, we organize de novo drug design into two overarching themes: small molecule and protein generation. Within each theme, we identify a variety of subtasks and applications, highlighting important datasets, benchmarks, and model architectures and comparing the performance of top models. We take a broad approach to AI-driven drug design, allowing for both micro-level comparisons of various methods within each subtask and macro-level observations across different fields. We discuss parallel challenges and approaches between the two applications and highlight future directions for AI-driven de novo drug design as a whole. An organized repository of all covered sources is available at https://github.com/gersteinlab/GenAI4Drug.
GTE: a graph learning framework for prediction of T-cell receptors and epitopes binding specificity
Authors: Jiang Feng , Guo Yuzhi , Ma Hehuan , Na Saiyang , Zhong Wenliang , Han Yi , Wang Tao , Huang Junzhou
Published: July 2024

The interaction between T-cell receptors (TCRs) and peptides (epitopes) presented by major histocompatibility complex molecules (MHC) is fundamental to the immune response. Accurate prediction of TCR–epitope interactions is crucial for advancing the understanding of various diseases and their prevention and treatment. Existing methods primarily rely on sequence-based approaches, overlooking the inherent topology structure of TCR–epitope interaction networks. In this study, we present $GTE$, a novel heterogeneous Graph neural network model based on inductive learning to capture the topological structure between TCRs and Epitopes. Furthermore, we address the challenge of constructing negative samples within the graph by proposing a dynamic edge update strategy, enhancing model learning with the nonbinding TCR–epitope pairs. Additionally, to overcome data imbalance, we adapt the Deep AUC Maximization strategy to the graph domain. Extensive experiments are conducted on four public datasets to demonstrate the superiority of exploring underlying topological structures in predicting TCR–epitope interactions, illustrating the benefits of delving into complex molecular networks. The implementation code and data are available at https://github.com/uta-smile/GTE.
A survey of experimental and computational identification of small proteins
Authors: Beals Joshua , Hu Haiyan , Li Xiaoman
Published: July 2024

Small proteins (SPs) are typically characterized as eukaryotic proteins shorter than 100 amino acids and prokaryotic proteins shorter than 50 amino acids. Historically, they were disregarded because of the arbitrary size thresholds to define proteins. However, recent research has revealed the existence of many SPs and their crucial roles. Despite this, the identification of SPs and the elucidation of their functions are still in their infancy. To pave the way for future SP studies, we briefly introduce the limitations and advancements in experimental techniques for SP identification. We then provide an overview of available computational tools for SP identification, their constraints, and their evaluation. Additionally, we highlight existing resources for SP research. This survey aims to initiate further exploration into SPs and encourage the development of more sophisticated computational tools for SP identification in prokaryotes and microbiomes.
Malignant paraganglioma of the prostate invading the bladder and bilateral seminal vesicles: a case report
Authors: Tao Jian , Ma Haiyan , Zeng Xianchun
Published: July 2024

Malignant paraganglioma (PGL) of the prostate is extremely rare, with only 3 cases reported in the English literature to date. In this article, we present a case of malignant prostatic PGL invading the bladder and bilateral seminal vesicles, in which the patient had a history of long-term haematuria and normal serum prostate specific antigen (PSA) level, and was misdiagnosed as a bladder tumour invading the prostate preoperatively. As this case belongs to functional tumour, there is a risk of developing hypertensive crisis during diagnostic biopsy or radical resection. The CT manifestations of prostatic PGL are characteristic, but its imaging features are rarely described due to the rarity of the tumour site. Meanwhile, improving the comprehensive understanding of CT, MRI, functional imaging, and clinical features of prostate PGL is conducive to make the correct diagnosis before surgery and ensure the safety of surgical treatment.
The graded multidimensional geometry of phenotypic variation and progression in neurodegenerative syndromes
Authors: Ramanan Siddharth , Akarca Danyal , Henderson Shalom K , Rouse Matthew A , Allinson Kieren , Patterson Karalyn , Rowe James B , Lambon Ralph Matthew A
Published: July 2024

Clinical variants of Alzheimer’s disease and frontotemporal lobar degeneration display a spectrum of cognitive-behavioural changes varying between individuals and over time. Understanding the landscape of these graded individual/group level longitudinal variations is critical for precise phenotyping; however, this remains challenging to model.

Addressing this challenge, we leverage the National Alzheimer’s Coordinating Center database to derive a unified geometric framework of graded longitudinal phenotypic variation in Alzheimer’s disease and frontotemporal lobar degeneration. We included three time point, cognitive-behavioural and clinical data from 390 typical, atypical and intermediate Alzheimer’s disease and frontotemporal lobar degeneration variants (114 typical Alzheimer’s disease; 107 behavioural variant frontotemporal dementia; 42 motor variants of frontotemporal lobar degeneration; and 103 primary progressive aphasia patients). On these data, we applied advanced data-science approaches to derive low-dimensional geometric spaces capturing core features underpinning clinical progression of Alzheimer’s disease and frontotemporal lobar degeneration syndromes.

To do so, we first used principal component analysis to derive six axes of graded longitudinal phenotypic variation capturing patient-specific movement along and across these axes. Then, we distilled these axes into a visualizable 2D manifold of longitudinal phenotypic variation using Uniform Manifold Approximation and Projection. Both geometries together enabled the assimilation and interrelation of paradigmatic and mixed cases, capturing dynamic individual trajectories and linking syndromic variability to neuropathology and key clinical end points, such as survival.

Through these low-dimensional geometries, we show that (i) specific syndromes (Alzheimer’s disease and primary progressive aphasia) converge over time into a de-differentiated pooled phenotype, while others (frontotemporal dementia variants) diverge to look different from this generic phenotype; (ii) phenotypic diversification is predicted by simultaneous progression along multiple axes, varying in a graded manner between individuals and syndromes; and (iii) movement along specific principal axes predicts survival at 36 months in a syndrome-specific manner and in individual pathological groupings. The resultant mapping of dynamics underlying cognitive-behavioural evolution potentially holds paradigm-changing implications to predicting phenotypic diversification and phenotype-neurobiological mapping in Alzheimer’s disease and frontotemporal lobar degeneration.
Modulation of the intermolecular interactions of cucurbit[7]uril with phenylalanine derivatives by the functional groups
Authors: Ueno-Noto Kaori , Toyama Seina , Kono Yuki , Takano Keiko
Published: July 2024

Intermolecular interactions in 1:1 inclusion complexes of cucurbit[7]uril (CB[7]) with phenylalanine derivatives were investigated by density functional theory (B97-D) calculations. For each complex, 2 optimized geometries were found: conformer C in which a guest molecule resided in the center of CB[7], and conformer E where a guest molecule was present at the edge of CB[7]. The order of energy differences between these conformers agreed well with previously reported differences in the affinity of guest molecules for CB[7]. Molecular dynamics simulations of the complexes showed that the guest molecules in CB[7] had different stabilities, and the calculated binding free energies between them also qualitatively agreed with the experimental results. Pair-interaction energy decomposition analyses of the complexes at FMO-MP2/6-31G(d) and aug-cc-pVDZ level of theory were performed using snapshot structures at 500 ns of simulations. The dispersion interaction characterized the interaction, and the order of total interaction energies between the guest molecules and CB[7] was also associated with the experimental results. A significant difference in electrostatic interaction energies was observed in conformer E, which was correlated with the stability of the guest molecules at the edge of CB[7]. The balance between the stabilities of these conformers was correlated with the affinity of guest molecules for CB[7].
Restorative justice in Brazil: does it provide a place for community involvement and a path to penal abolition?
Authors: Achutti Daniel , Pallamolla Raffaella , Giamberardino André
Published: July 2024

This article addresses the major criticisms of Brazilian restorative practices, which mainly focus on the offender and are shaped by the idea of punitivism. In this scenario, it is crucial to understand the centrality of Judicial Power in the implementation of restorative justice. That this approach risks refreshing old practices of criminal justice, under the cover of innovative discourses, is widely ignored. Such consequences have become reality, with recent research highlighting the absence of the victim, the individualization of the conflict and the lack of debate on the context of structural injustices prior to the conflict. We argue that the exclusion of the community and limited involvement by civil society might be the biggest obstacles for the inclusion of restorative justice in the development of a Brazilian transformative justice towards an abolitionist future.
Trichophyton indotineae: first case in Ireland and response to topical griseofulvin
Authors: Carroll Emma , Leahy Marion , Stanciu Maria , Laing Mary
Published: July 2024

To our knowledge, we report the first case of Trichophyton indotineae in Ireland, highlighting the pathogen’s resistance to conventional antifungal treatments and the necessity for advanced diagnostic techniques. Notably, the infection in our patient began to resolve when griseofulvin liquid was unintentionally used topically, suggesting an alternative treatment approach for this resistant dermatophyte.
Insular environment-dependent introgression from an arid-grassland orchid to a wetland orchid on an oceanic island
Authors: Suetsugu Kenji , Hirota Shun K , Ishibashi Masayuki , Ishida Kenya , Hayakawa Hiroshi , Suyama Yoshihisa
Published: July 2024

Adaptive introgression plays a vital role in allowing recipient species to adapt and colonize new environments. However, our understanding of such environment-dependent introgressions is primarily limited to specific plant taxa in particular settings. In Japan, two related orchid species, the autonomously self-pollinating Pogonia minor and the outcrossing Pogonia japonica, typically inhabit dry grasslands and wetlands, respectively. Intriguingly, an island ecotype of P. japonica exists in arid, wind-swept, open sites on volcanic mountain slopes on Kozu Island, in the oceanic Izu Islands. To investigate potential introgression and its implications between P. japonica and P. minor on Kozu Island, we applied a comprehensive approach that included examining morphological traits, genome-wide SNP data, and plastid DNA sequences. We also examined the breeding systems of these species on Kozu Island through artificial pollination experiments to determine if introgression from P. minor has endowed the P. japonica ecotype with selfing capabilities. Extensive sampling on Kozu Island revealed that all P. japonica specimens exhibit signs of introgression from P. minor, suggesting the absence of pure P. japonica populations on the island. Furthermore, the chloroplast haplotypes of the insular P. japonica ecotype consistently match those of P. minor, indicating a predominantly asymmetrical initial hybridization with P. minor acting mainly as the maternal parent in the formation of F1 hybrids. Despite the advantages of self-fertilization in isolated environments, the insular P. japonica does not exhibit autogamy. Consequently, the scarcity of moist habitats, rather than selection pressure for selfing, likely contributes to the observed widespread introgression. Our study strongly suggests that the arid-environment-adapted P. minor has introgressed into the insular ecotype of P. japonica, enabling its successful colonization of arid volcanic mountain slopes of the oceanic island.
Chk2 homolog Mek1 limits exonuclease 1–dependent DNA end resection during meiotic recombination in Saccharomyces cerevisiae
Authors: Krystosek Jennifer T , Bishop Douglas K
Published: July 2024

The conserved Rad2/XPG family 5′–3′ exonuclease, exonuclease 1 (Exo1), plays many roles in DNA metabolism including during resolution of DNA double-strand breaks via homologous recombination. Prior studies provided evidence that the end resection activity of Exo1 is downregulated in yeast and mammals by Cdk1/2 family cyclin-dependent and checkpoint kinases, including budding yeast kinase Rad53 which functions in mitotic cells. Here, we provide evidence that the master meiotic kinase Mek1, a paralog of Rad53, limits 5′–3′ single-strand resection at the sites of programmed meiotic DNA breaks. Mutational analysis suggests that the mechanism of Exo1 suppression by Mek1 differs from that of Rad53.
Restorer of fertility like 30, encoding a mitochondrion-localized pentatricopeptide repeat protein, regulates wood formation in poplar
Authors: Fu Xiaokang , Yang Ziwei , Guo Li , Luo Lianjia , Tao Yuanxun , Lan Ting , Hu Jian , Li Zeyu , Luo Keming , Xu Changzheng
Published: July 2024

Nuclear–mitochondrial communication is crucial for plant growth, particularly in the context of cytoplasmic male sterility (CMS) repair mechanisms linked to mitochondrial genome mutations. The restorer of fertility-like (RFL) genes, known for their role in CMS restoration, remain largely unexplored in plant development. In this study, we focused on the evolutionary relationship of RFL family genes in poplar specifically within the dioecious Salicaceae plants. PtoRFL30 was identified to be preferentially expressed in stem vasculature, suggesting a distinct correlation with vascular cambium development. Transgenic poplar plants overexpressing PtoRFL30 exhibited a profound inhibition of vascular cambial activity and xylem development. Conversely, RNA interference-mediated knockdown of PtoRFL30 led to increased wood formation. Importantly, we revealed that PtoRFL30 plays a crucial role in maintaining mitochondrial functional homeostasis. Treatment with mitochondrial activity inhibitors delayed wood development in PtoRFL30-RNAi transgenic plants. Further investigations unveiled significant variations in auxin accumulation levels within vascular tissues of PtoRFL30-transgenic plants. Wood development anomalies resulting from PtoRFL30 overexpression and knockdown were rectified by NAA and NPA treatments, respectively. Our findings underscore the essential role of the PtoRFL30-mediated mitochondrion-auxin signaling module in wood formation, shedding light on the intricate nucleus–organelle communication during secondary vascular development.
Prospective evaluation of the relevance of Epstein–Barr virus antibodies for early detection of nasopharyngeal carcinoma in Chinese adults
Authors: Yang Ling , Kartsonaki Christiana , Simon Julia , Yao Pang , Guo Yu , Lv Jun , Walters Robin G , Chen Yiping , Fry Hannah , Avery Daniel , Yu Canqing , Jin Jianrong , Mentzer Alexander J , Allen Naomi , Butt Julia , Hill Michael , Li Liming , Millwood Iona Y , Waterboer Tim , Chen Zhengming
Published: July 2024

Background

Epstein–Barr virus (EBV) is a major cause of nasopharyngeal carcinoma (NPC) and measurement of different EBV antibodies in blood may improve early detection of NPC. Prospective studies can help assess the roles of different EBV antibodies in predicting NPC risk over time.

Methods

A case-cohort study within the prospective China Kadoorie Biobank of 512 715 adults from 10 (including two NPC endemic) areas included 295 incident NPC cases and 745 subcohort participants. A multiplex serology assay was used to quantify IgA and IgG antibodies against 16 EBV antigens in stored baseline plasma samples. Cox regression was used to estimate adjusted hazard ratios (HRs) for NPC and C-statistics to assess the discriminatory ability of EBV-markers, including two previously identified EBV-marker combinations, for predicting NPC.

Results

Sero-positivity for 15 out of 16 EBV-markers was significantly associated with higher NPC risk. Both IgA and IgG antibodies against the same three EBV-markers showed the most extreme HRs, i.e. BGLF2 (IgA: 124.2 (95% CI: 63.3–243.9); IgG: 8.6 (5.5–13.5); LF2: [67.8 (30.0–153.1), 10.9 (7.2–16.4)]); and BFRF1: 26.1 (10.1–67.5), 6.1 (2.7–13.6). Use of a two-marker (i.e. LF2/BGLF2 IgG) and a four-marker (i.e. LF2/BGLF2 IgG and LF2/EA-D IgA) combinations yielded C-statistics of 0.85 and 0.84, respectively, which persisted for at least 5 years after sample collection in both endemic and non-endemic areas.

Conclusions

In Chinese adults, plasma EBV markers strongly predict NPC occurrence many years before clinical diagnosis. LF2 and BGLF2 IgG could identify NPC high-risk individuals to improve NPC early detection in community and clinical settings.
Generative early architectural visualizations: incorporating architect’s style-trained models
Authors: Lee Jin-Kook , Yoo Youngjin , Cha Seung Hyun
Published: July 2024

This study introduces a novel approach to architectural visualization using generative artificial intelligence (AI), particularly emphasizing text-to-image technology, to remarkably improve the visualization process right from the initial design phase within the architecture, engineering, and construction industry. By creating more than 10 000 images incorporating an architect’s personal style and characteristics into a residential house model, the effectiveness of base AI models. Furthermore, various architectural styles were integrated to enhance the visualization process. This method involved additional training for styles with low similarity rates, which required extensive data preparation and their integration into the base AI model. Demonstrated to be effective across multiple scenarios, this technique markedly enhances the efficiency and speed of production of architectural visualization images. Highlighting the vast potential of AI in design visualization, our study emphasizes the technology’s shift toward facilitating more user-centered and personalized design applications.
A genome assembly of the American black bear, Ursus americanus, from California
Authors: Supple Megan A , Escalona Merly , Adkins Jillian , Buchalski Michael R , Alexandre Nicolas , Sahasrabudhe Ruta M , Nguyen Oanh , Sacco Samuel , Fairbairn Colin , Beraut Eric , Seligmann William , Green Richard E , Meredith Erin , Shapiro Beth
Published: July 2024

The American black bear, Ursus americanus, is a widespread and ecologically important species in North America. In California, the black bear plays an important role in a variety of ecosystems and serves as an important species for recreational hunting. While research suggests that the populations in California are currently healthy, continued monitoring is critical, with genomic analyses providing an important surveillance tool. Here we report a high-quality, near chromosome-level genome assembly from a U. americanus sample from California. The primary assembly has a total length of 2.5 Gb contained in 316 scaffolds, a contig N50 of 58.9 Mb, a scaffold N50 of 67.6 Mb, and a BUSCO completeness score of 96%. This U. americanus genome assembly will provide an important resource for the targeted management of black bear populations in California, with the goal of achieving an appropriate balance between the recreational value of black bears and the maintenance of viable populations. The high quality of this genome assembly will also make it a valuable resource for comparative genomic analyses among black bear populations and among bear species.
Nasopharyngeal methicillin-resistant Staphylococcus aureus carriage among pilgrims at the Grand Magal de Touba
Authors: Ouaddane Ihssane , Diouf Coumba , Goumballa Ndiaw , Hoang Van-Thuan , Zinai Amira Zhor Rim , Sokhna Cheikh , Gautret Philippe
Published: July 2024

Overall prevalence of nasopharyngeal methicillin-resistant Staphylococcus aureus (MRSA) carriage in Grand Magal de Touba pilgrims was 5.2% by PCR and 2.6% acquired carriage following participation in the event. Given the potential for globalization of pathogens, surveillance is crucial to implementing timely interventions and protecting public health during the mass gathering.
The diagnostic value of pleural effusion/serum ratio of carcinoembryonic antigen and pleural effusion/serum ratio of interferon-γ in classification of pleural effusion
Authors: Liang Shu-hui , Li Cui , Xie Si
Published: July 2024

Background

Distinguishing between different types of pleural effusions (PEs) is crucial for clinical diagnosis and treatment. This study evaluates the diagnostic value of carcinoembryonic antigen (CEA) and interferon-gamma (IFN-γ) levels in PE and serum, as well as the PE/serum ratios of these markers, in classifying PE.

Methods

We retrospectively analyzed 99 patients with PE, categorizing them into malignant pleural effusion (MPE), tuberculous pleural effusion (TPE), and benign PE groups. Levels of CEA and IFN-γ in PE and serum were quantified and their ratios were calculated. Diagnostic performance was assessed using receiver operating characteristic analysis, focusing on the area under the curve (AUC) to determine the efficacy of these biomarkers.

Results

Significantly elevated levels of CEA in PE and serum were observed in the MPE group compared to the benign and TPE groups, with the PE/serum CEA ratio offering substantial diagnostic value (AUCs: PE = 0.843, serum = 0.744). Conversely, IFN-γ levels in PE and serum were markedly higher in the TPE group, demonstrating notable diagnostic accuracy (AUCs: PE = 0.970, serum = 0.917).

Conclusion

Both CEA and IFN-γ demonstrate high clinical utility in differentiating between MPE and TPE. The PE/serum ratio of these biomarkers enhances diagnostic accuracy, potentially facilitating earlier and more accurate therapeutic interventions.
Investigating the antimicrobial potential of bovine lactoferrin against the neonatal pathogen, Staphylococcus capitis
Authors: Desmond Anna , Cotter Lesley , Field Des , O'Halloran Fiona
Published: July 2024

Lactoferrin is an antimicrobial glycoprotein that demonstrates a broad-spectrum of activity against a wide variety of clinical pathogens. This study investigated the potential of bovine lactoferrin (bLf) against multidrug resistant Staphylococcus capitis (S. capitis) strains. Growth curve analysis and time-kill curves demonstrated that at 750 µg ml−1 lactoferrin significantly inhibited (50.6%, P < 0.05) the growth of most isolates tested (90%), and this effect was based on a bacteriostatic mechanism. At the same concentration, bLf also significantly inhibited (30%, P < 0.05) biofilm formation in 40% of strains tested. Combinations of bLf with selected antibiotics were assessed for enhanced antimicrobial activity using growth curves. BLf combined with β-lactam antibiotics reduced the growth of S. capitis strains, however, the effects were not significant. BLf displays antimicrobial effects against multidrug resistant S. capitis isolates, but with strain-specific effects.