bluuebunny/crossref_metadata_2025_split huggingface dataset:
Giant Dzyaloshinskii-Moriya interaction, strong XXZ-type biquadratic coupling, and bimeronic excitations in the two-dimensional CrMnI6 magnet
Authors: Zhang Shunhong , Li Xiaoyin , Zhang Huisheng , Cui Ping , Xu Xiaohong , Zhang Zhenyu 
Published: July 2023

AbstractTwo-dimensional magnets have been discovered recently as a new class of quantum matter exhibiting a broad wealth of exotic phenomena, including notably various topological excitations rooted in emergent exchange couplings between the localized magnetic moments. By analyzing the anisotropies in the single-ion magnetization and two-body exchange couplings obtained from first-principles calculations, we reveal coexistence of both giant Dzyaloshinskii–Moriya interaction and strong anisotropic XXZ-type biquadratic coupling in a recently predicted monolayer CrMnI6 magnet. The former is induced by the spontaneous in-plane inversion symmetry breaking in the bipartite system, the latter is inherently tied to the distinct high-spin state of the Mn sublattice, while the large magnitudes of both stem from the significant spin-orbit coupling. Next, we use atomistic magnetics simulations to demonstrate the vital role of Dzyaloshinskii–Moriya interaction in harboring topological bimeronic excitations, and show that the biquadratic coupling favors a Berezinskii–Kosterlitz–Thouless-like transition as the system reduces its temperature from the paramagnetic phase. These findings substantially enrich our understanding of the microscopic couplings in 2D magnets, with appealing application potentials.
Global nitrogen deposition inputs to cropland at national scale from 1961 to 2020
Authors: Vishwakarma Srishti , Zhang Xin , Dobermann Achim , Heffer Patrick , Zhou Feng 
Published: July 2023

AbstractNitrogen (N) deposition is a significant nutrient input to cropland and consequently important for the evaluation of N budgets and N use efficiency (NUE) at different scales and over time. However, the spatiotemporal coverage of N deposition measurements is limited globally, whereas modeled N deposition values carry uncertainties. Here, we reviewed existing methods and related data sources for quantifying N deposition inputs to crop production on a national scale. We utilized different data sources to estimate N deposition input to crop production at national scale and compared our estimates with 14 N budget datasets, as well as measured N deposition data from observation networks in 9 countries. We created four datasets of N deposition inputs on cropland during 1961–2020 for 236 countries. These products showed good agreement for the majority of countries and can be used in the modeling and assessment of NUE at national and global scales. One of the datasets is recommended for general use in regional to global N budget and NUE estimates.
AtOM, an ontology model to standardize use of brain atlases in tools, workflows, and data infrastructures
Authors: Kleven Heidi , Gillespie Thomas H. , Zehl Lyuba , Dickscheid Timo , Bjaalie Jan G. , Martone Maryann E. , Leergaard Trygve B. 
Published: July 2023

AbstractBrain atlases are important reference resources for accurate anatomical description of neuroscience data. Open access, three-dimensional atlases serve as spatial frameworks for integrating experimental data and defining regions-of-interest in analytic workflows. However, naming conventions, parcellation criteria, area definitions, and underlying mapping methodologies differ considerably between atlases and across atlas versions. This lack of standardized description impedes use of atlases in analytic tools and registration of data to different atlases. To establish a machine-readable standard for representing brain atlases, we identified four fundamental atlas elements, defined their relations, and created an ontology model. Here we present our Atlas Ontology Model (AtOM) and exemplify its use by applying it to mouse, rat, and human brain atlases. We discuss how AtOM can facilitate atlas interoperability and data integration, thereby increasing compliance with the FAIR guiding principles. AtOM provides a standardized framework for communication and use of brain atlases to create, use, and refer to specific atlas elements and versions. We argue that AtOM will accelerate analysis, sharing, and reuse of neuroscience data.
Air-quality prediction based on the ARIMA-CNN-LSTM combination model optimized by dung beetle optimizer
Authors: Duan Jiahui , Gong Yaping , Luo Jun , Zhao Zhiyao 
Published: July 2023

AbstractAir pollution is a serious problem that affects economic development and people’s health, so an efficient and accurate air quality prediction model would help to manage the air pollution problem. In this paper, we build a combined model to accurately predict the AQI based on real AQI data from four cities. First, we use an ARIMA model to fit the linear part of the data and a CNN-LSTM model to fit the non-linear part of the data to avoid the problem of blinding in the CNN-LSTM hyperparameter setting. Then, to avoid the blinding dilemma in the CNN-LSTM hyperparameter setting, we use the Dung Beetle Optimizer algorithm to find the hyperparameters of the CNN-LSTM model, determine the optimal hyperparameters, and check the accuracy of the model. Finally, we compare the proposed model with nine other widely used models. The experimental results show that the model proposed in this paper outperforms the comparison models in terms of root mean square error (RMSE), mean absolute error (MAE) and coefficient of determination (R2). The RMSE values for the four cities were 7.594, 14.94, 7.841 and 5.496; the MAE values were 5.285, 10.839, 5.12 and 3.77; and the R2 values were 0.989, 0.962, 0.953 and 0.953 respectively.
Histone deacetylase inhibitors inhibit lung adenocarcinoma metastasis via HDAC2/YY1 mediated downregulation of Cdh1
Authors: Wang Dongmei , Yang Yixiao , Cao Yuxiang , Meng Meiyao , Wang Xiaobo , Zhang Zhengxun , Fu Wei , Duan Shichao , Tang Liming 
Published: July 2023

AbstractMetastasis is a leading cause of mortality in patients with lung adenocarcinoma. Histone deacetylases have emerged as promising targets for anti-tumor drugs, with histone deacetylase inhibitors (HDACi) being an active area of research. However, the precise mechanisms by which HDACi inhibits lung cancer metastasis remain incompletely understood. In this study, we employed a range of techniques, including qPCR, immunoblotting, co-immunoprecipitation, chromatin-immunoprecipitation, and cell migration assays, in conjunction with online database analysis, to investigate the role of HDACi and HDAC2/YY1 in the process of lung adenocarcinoma migration. The present study has demonstrated that both trichostatin A (TSA) and sodium butyrate (NaBu) significantly inhibit the invasion and migration of lung cancer cells via Histone deacetylase 2 (HDAC2). Overexpression of HDAC2 promotes lung cancer cell migration, whereas shHDAC2 effectively inhibits it. Further investigation revealed that HDAC2 interacts with YY1 and deacetylates Lysine 27 and Lysine9 of Histone 3, thereby inhibiting Cdh1 transcriptional activity and promoting cell migration. These findings have shed light on a novel functional mechanism of HDAC2/YY1 in lung adenocarcinoma cell migration.
Dosage of the pseudoautosomal gene SLC25A6 is implicated in QTc interval duration
Authors: Skakkebæk Anne , Kjær-Sørensen Kasper , Matchkov Vladimir V. , Christensen Lise-Lotte , Just Jesper , Cömert Cagla , Andersen Niels Holmark , Oxvig Claus , Gravholt Claus Højbjerg 
Published: July 2023

AbstractThe genetic architecture of the QT interval, defined as the period from onset of depolarisation to completion of repolarisation of the ventricular myocardium, is incompletely understood. Only a minor part of the QT interval variation in the general population has been linked to autosomal variant loci. Altered X chromosome dosage in humans, as seen in sex chromosome aneuploidies such as Turner syndrome (TS) and Klinefelter syndrome (KS), is associated with altered QTc interval (heart rate corrected QT), indicating that genes, located in the pseudoautosomal region 1 of the X and Y chromosomes may contribute to QT interval variation. We investigate the dosage effect of the pseudoautosomal gene SLC25A6, encoding the membrane ADP/ATP translocase 3 in the inner mitochondrial membrane, on QTc interval duration. To this end we used human participants and in vivo zebrafish models. Analyses in humans, based on 44 patients with KS, 44 patients with TS, 59 male and 22 females, revealed a significant negative correlation between SLC25A6 expression level and QTc interval duration. Similarly, downregulation of slc25a6 in zebrafish increased QTc interval duration with pharmacological inhibition of KATP channels restoring the systolic duration, whereas overexpression of SLC25A6 shortened QTc, which was normalized by pharmacological activation of KATP channels. Our study demonstrate an inverse relationship between SLC25A6 dosage and QTc interval indicating that SLC25A6 contributes to QT interval variation.
Effects of N and P addition on nutrient and stoichiometry of rhizosphere and non-rhizosphere soils of alfalfa in alkaline soil
Authors: Gu Xudong , Zhang Fengju , Xie Xiaowei , Cheng Yunlong , Xu Xing 
Published: July 2023

AbstractNitrogen (N) and phosphorus (P) are important nutrients for plant growth and development. Soil alkalization is one of the main obstacles limiting the sustainable development of agriculture. Northern Ningxia is located in the arid and semi-arid region, with serious soil alkalinization. Alfalfa has the advantages of strong saline-alkali tolerance, high yield, high quality, and wide adaptability. It is an important forage for the comprehensive improvement and rational utilization of saline-alkali land and has great significance for solving land resource shortages, improving the ecological environment, and ensuring food security. It is important to study soil organic carbon (SOC), total N (TN), total P (TP), and stoichiometry of the rhizosphere and non-rhizosphere of alfalfa in alkaline soils. Therefore, N and P were added to the alkaline alfalfa field in the Yinchuan Plain of Hetao Basin in our experiment. Six treatments were set up, i.e., N-free (WN), medium N (MN) for 90 kg/hm2, high N (HN) for 180 kg/hm2, P-free (WP), medium P (MP) for 135 kg/hm2, and high P (HP) for 270 kg/hm2. The results are as follows: The N addition promotes SOC and TN but inhibits TP, and P addition promotes SOC and TP but inhibits TN of three soil layers. The N addition decreases C/N but increases C/P and N/P, while the P addition increases C/N but decreases C/P and N/P of three soil layers. The SOC, TN, TP, C/N, C/P, and N/P under HN and HP treatment reach the significance level (P < 0.05). Appropriate additions of N and P can improve rhizosphere and non-rhizosphere nutrients and stoichiometric structure, facilitating absorption and utilization by alfalfa and improve the production potential of alfalfa in alkaline soil.
Standardized assessment of vascular reconstruction kernels in photon-counting CT angiographies of the leg using a continuous extracorporeal perfusion model
Authors: Gruschwitz Philipp , Hartung Viktor , Kleefeldt Florian , Ergün Süleyman , Lichthardt Sven , Huflage Henner , Hendel Robin , Kunz Andreas Steven , Pannenbecker Pauline , Kuhl Philipp Josef , Augustin Anne Marie , Bley Thorsten Alexander , Petritsch Bernhard , Grunz Jan-Peter 
Published: July 2023

AbstractThis study evaluated the influence of different vascular reconstruction kernels on the image quality of CT angiographies of the lower extremity runoff using a 1st-generation photon-counting-detector CT (PCD-CT) compared with dose-matched examinations on a 3rd-generation energy-integrating-detector CT (EID-CT). Inducing continuous extracorporeal perfusion in a human cadaveric model, we performed CT angiographies of eight upper leg arterial runoffs with radiation dose-equivalent 120 kVp acquisition protocols (CTDIvol 5 mGy). Reconstructions were executed with different vascular kernels, matching the individual modulation transfer functions between scanners. Signal-to-noise-ratios (SNR) and contrast-to-noise-ratios (CNR) were computed to assess objective image quality. Six radiologists evaluated image quality subjectively using a forced-choice pairwise comparison tool. Interrater agreement was determined by calculating Kendall’s concordance coefficient (W). The intraluminal attenuation of PCD-CT images was significantly higher than of EID-CT (414.7 ± 27.3 HU vs. 329.3 ± 24.5 HU; p < 0.001). Using comparable kernels, image noise with PCD-CT was significantly lower than with EID-CT (p ≤ 0.044). Correspondingly, SNR and CNR were approximately twofold higher for PCD-CT (p < 0.001). Increasing the spatial frequency for PCD-CT reconstructions by one level resulted in similar metrics compared to EID-CT (CNRfat; EID-CT Bv49: 21.7 ± 3.7 versus PCD-CT Bv60: 21.4 ± 3.5). Overall image quality of PCD-CTA achieved ratings superior to EID-CTA irrespective of the used reconstruction kernels (best: PCD-CT Bv60; worst: EID-CT Bv40; p < 0.001). Interrater agreement was good (W = 0.78). Concluding, PCD-CT offers superior intraluminal attenuation, SNR, and CNR compared to EID-CT in angiographies of the upper leg arterial runoff. Combined with improved subjective image quality, PCD-CT facilitates the use of sharper convolution kernels and ultimately bears the potential of improved vascular structure assessability.
Investigation of the rate-mediated form-function relationship in biological puncture
Authors: Zhang Bingyang , Anderson Philip S. L. 
Published: July 2023

AbstractPuncture is a vital mechanism for survival in a wide range of organisms across phyla, serving biological functions such as prey capture, defense, and reproduction. Understanding how the shape of the puncture tool affects its functional performance is crucial to uncovering the mechanics underlying the diversity and evolution of puncture-based systems. However, such form-function relationships are often complicated by the dynamic nature of living systems. Puncture systems in particular operate over a wide range of speeds to penetrate biological tissues. Current studies on puncture biomechanics lack systematic characterization of the complex, rate-mediated, interaction between tool and material across this dynamic range. To fill this knowledge gap, we establish a highly controlled experimental framework for dynamic puncture to investigate the relationship between the puncture performance (characterized by the depth of puncture) and the tool sharpness (characterized by the cusp angle) across a wide range of bio-relevant puncture speeds (from quasi-static to $$\sim$$
∼
50 m/s). Our results show that the sensitivity of puncture performance to variations in tool sharpness reduces at higher puncture speeds. This trend is likely due to rate-based viscoelastic and inertial effects arising from how materials respond to dynamic loads. The rate-dependent form-function relationship has important biological implications: While passive/low-speed puncture organisms likely rely heavily on sharp puncture tools to successfully penetrate and maintain functionalities, higher-speed puncture systems may allow for greater variability in puncture tool shape due to the relatively geometric-insensitive puncture performance, allowing for higher adaptability during the evolutionary process to other mechanical factors.
Prospective study to evaluate quality of life in amyotrophic lateral sclerosis
Authors: Caballero-Eraso Candela , Carrera-Cueva Carlos , de Benito Zorrero Esther , Lopez-Ramirez Cecilia , Marin-Romero Samira , Asensio-Cruz Maria Isabel , Barrot-Cortes Emilia , Jara-Palomares Luis 
Published: July 2023

AbstractAmyotrophic lateral sclerosis (ALS) is a neurodegenerative rare disease characterized by symptoms and signs in the upper and lower motor neurons, leading to progressive neuro-degeneration and muscle atrophy. Our objective was to analyse the quality of life (QoL) in patients with ALS and compare with general population and with patients with cancer. Prospective study from consecutive ALS patients in one center. In order to assess quality of life, during the first visit three questionnaires were administered: Amyotrophic Lateral Sclerosis Functional Rating Scale (ALSFRS-R), Short Form-36 (SF-36) and EuroQoL 5D (EQ-5D). We compared SF-36 of ALS patients with a reference population (n = 9151), and we compared the EQ-5D index score of ALS patients versus patients with cancer in the same area and in the same period (2015–2018). Between June 2015 and September 2017, 23 were included. The mean age was 65.1 ± 12.6 years and 56.5% were women. Compared with the general population, patients with ALS showed lowest QoL (p < 0.05) in all the dimensions, with a very important impairment in physical function (median: 0; p25-75: 0–10) and physical role (median: 0; p25-75: 0–6.25). In EQ-5D questionnaire, patients with ALS presented an EQ-5D index score of 0.21 ± 0.39 (mean ± standard deviation) with a visual analog scale (VAS) score of 0.32 ± 0.24. Compared with an oncological population, patients with ALS had a worse EQ-5D index score both clinically and statistically (0.21 ± 0.39 vs. 0.77 ± 0.27; p < 0.05). We demonstrate a poorer quality of life in patients with ALS is poor, and clinically and statistically worse than in patients with cancer or general population. New studies need to evaluate the impact of strategies in this population to improve the quality of life.
A novel approach to finding conserved features in low-variability gene alignments characterises RNA motifs in SARS-CoV and SARS-CoV-2
Authors: Skittrall Jordan P. , Irigoyen Nerea , Brierley Ian , Gog Julia R. 
Published: July 2023

AbstractCollections of genetic sequences belonging to related organisms contain information on the evolutionary constraints to which the organisms have been subjected. Heavily constrained regions can be investigated to understand their roles in an organism’s life cycle, and drugs can be sought to disrupt these roles. In organisms with low genetic diversity, such as newly-emerged pathogens, it is key to obtain this information early to develop new treatments. Here, we present methods that ensure we can leverage all the information available in a low-signal, low-noise set of sequences, to find contiguous regions of relatively conserved nucleic acid. We demonstrate the application of these methods by analysing over 5 million genome sequences of the recently-emerged RNA virus SARS-CoV-2 and correlating these results with an analysis of 119 genome sequences of SARS-CoV. We propose the precise location of a previously described packaging signal, and discuss explanations for other regions of high conservation.
Identification of metabolic pathways contributing to ER+ breast cancer disparities using a machine-learning pipeline
Authors: Santaliz-Casiano Ashlie , Mehta Dhruv , Danciu Oana C. , Patel Hariyali , Banks Landan , Zaidi Ayesha , Buckley Jermya , Rauscher Garth H. , Schulte Lauren , Weller Lauren Ro , Taiym Deanna , Liko-Hazizi Elona , Pulliam Natalie , Friedewald Sarah M. , Khan Seema , Kim J. Julie , Gradishar William , Hegerty Scott , Frasor Jonna , Hoskins Kent F. , Madak-Erdogan Zeynep 
Published: July 2023

AbstractAfrican American (AA) women in the United States have a 40% higher breast cancer mortality rate than Non-Hispanic White (NHW) women. The survival disparity is particularly striking among (estrogen receptor positive) ER+ breast cancer cases. The purpose of this study is to examine whether there are racial differences in metabolic pathways typically activated in patients with ER+ breast cancer. We collected pretreatment plasma from AA and NHW ER+ breast cancer cases (AA n = 48, NHW n = 54) and cancer-free controls (AA n = 100, NHW n = 48) to conduct an untargeted metabolomics analysis using gas chromatography mass spectrometry (GC–MS) to identify metabolites that may be altered in the different racial groups. Unpaired t-test combined with multiple feature selection and prediction models were employed to identify race-specific altered metabolic signatures. This was followed by the identification of altered metabolic pathways with a focus in AA patients with breast cancer. The clinical relevance of the identified pathways was further examined in PanCancer Atlas breast cancer data set from The Cancer Genome Atlas Program (TCGA). We identified differential metabolic signatures between NHW and AA patients. In AA patients, we observed decreased circulating levels of amino acids compared to healthy controls, while fatty acids were significantly higher in NHW patients. By mapping these metabolites to potential epigenetic regulatory mechanisms, this study identified significant associations with regulators of metabolism such as methionine adenosyltransferase 1A (MAT1A), DNA Methyltransferases and Histone methyltransferases for AA individuals, and Fatty acid Synthase (FASN) and Monoacylglycerol lipase (MGL) for NHW individuals. Specific gene Negative Elongation Factor Complex E (NELFE) with histone methyltransferase activity, was associated with poor survival exclusively for AA individuals. We employed a comprehensive and novel approach that integrates multiple machine learning and statistical methods, coupled with human functional pathway analyses. The metabolic profile of plasma samples identified may help elucidate underlying molecular drivers of disproportionately aggressive ER+ tumor biology in AA women. It may ultimately lead to the identification of novel therapeutic targets. To our knowledge, this is a novel finding that describes a link between metabolic alterations and epigenetic regulation in AA breast cancer and underscores the need for detailed investigations into the biological underpinnings of breast cancer health disparities.
Adaptive group testing strategy for infectious diseases using social contact graph partitions
Authors: Zhang Jingyi , Heath Lenwood S. 
Published: July 2023

AbstractMass testing is essential for identifying infected individuals during an epidemic and allowing healthy individuals to return to normal social activities. However, testing capacity is often insufficient to meet global health needs, especially during newly emerging epidemics. Dorfman’s method, a classic group testing technique, helps reduce the number of tests required by pooling the samples of multiple individuals into a single sample for analysis. Dorfman’s method does not consider the time dynamics or limits on testing capacity involved in infection detection, and it assumes that individuals are infected independently, ignoring community correlations. To address these limitations, we present an adaptive group testing (AGT) strategy based on graph partitioning, which divides a physical contact network into subgraphs (groups of individuals) and assigns testing priorities based on the social contact characteristics of each subgraph. Our AGT aims to maximize the number of infected individuals detected and minimize the number of tests required. After each testing round (perhaps on a daily basis), the testing priority is increased for each neighboring group of known infected individuals. We also present an enhanced infectious disease transmission model that simulates the dynamic spread of a pathogen and evaluate our AGT strategy using the simulation results. When applied to 13 social contact networks, AGT demonstrates significant performance improvements compared to Dorfman’s method and its variations. Our AGT strategy requires fewer tests overall, reduces disease spread, and retains robustness under changes in group size, testing capacity, and other parameters. Testing plays a crucial role in containing and mitigating pandemics by identifying infected individuals and helping to prevent further transmission in families and communities. By identifying infected individuals and helping to prevent further transmission in families and communities, our AGT strategy can have significant implications for public health, providing guidance for policymakers trying to balance economic activity with the need to manage the spread of infection.