bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of hub genes and biological process analysis of otosclerosis patients based on WGCNA analysis
Authors: Wang Wei , Zhang Dongdong , Lei Min , Wang Yue , Zeng Peiji , Zou Cong , Hong Yongjun , Cai Chengfu 
Published: April 2023

Abstract
Background： Otosclerosis is a primary bone disease caused by the bone labyrinth, resorption, and abnormal bone deposition. According to current research, it is a complex disease related to genetic and environmental factors. However, the molecular mechanism associated with otosclerosis has not been clearly revealed.
Methods： The purpose of this study was to screen differentially expressed genes (DEGs) in otosclerosis patients and corresponding normal controls by RNA sequencing (RNA-Seq) and then deal with DEGS by weighted gene co-expression network analysis (WGCNA). Gene ontology (GO) enrichment, Kyoto Encyclopedia of Gene and Genome (KEGG) pathway enrichment analysis are used to analyze genes in modules of clinical significance.
Results： We obtained 11 modules of WGCNA and identified turquoise modules with 184 genes, which were highly related to the phenotype (otosclerosis) of WGCNA. Protein-protein interaction (PPI) network was constructed by using Cytoscape. GO analysis showed that the turquoise module was related to the transcriptional regulation of RNA polymerase II promoter, nucleus, and protein binding, while KEGG and PEA analysis showed that the turquoise module was mainly enriched in nucleocytoplasmic transport. We obtained 10 hub genes, which were verified by HPA (The Human Protein Atlas) database. Among them, AZU1, CAMP, and MPO were highly expressed in normal bone marrow tissues, while the expression in otosclerosis patients was significantly down-regulated compared with the control group.
Conclusion： This suggests that these molecules can be used as candidate markers to distinguish between otosclerosis patients and healthy people. Overall, our research shows that the three hub genes may play a key role in the occurrence and development of otosclerosis.
Group action on the set of non-units in rings
Authors: Almotairi Eman S. , Bhat M. Imran , Alghamdi Ahmad M. 
Published: April 2023

Abstract
Let R be a ring, G be the group of all units of R and X = R − G ∪ {0}. In this paper, we investigate |{av(x)|x ∈ X}| = |{o(x)|x ∈ X}| for a ring R, where av(x) is the set of all vertices of the zero-divisor graph of R adjacent to x. We also investigate the question on zero-divisor graphs posed by J. Han in 2010 [10]; when the equality e(≠ 0, 1), o(1 − e) = av(e) holds for any idempotent element e(≠ 0, 1) in a commutative regular ring R with identity.
AMS subject classification: 2020: 13A50, 05C25, 16W22
Mapping the planet's critical areas for biodiversity and people
Authors: Neugarten Rachel , Chaplin-Kramer Rebecca , Sharp Richard , Schuster Richard , Strimas-Mackey Matthew , Roehrdanz Patrick , Mulligan Mark , Soesbergen Arnout van , Hole David , Kennedy Christina , Oakleaf James , Johnson Justin , Kiesecker Joseph , Polasky Stephen , Hanson Jeffrey , Rodewald Amanda 
Published: April 2023

Abstract
Meeting global commitments to conservation, climate, and sustainable development goals requires consideration of synergies and tradeoffs among targets. We evaluate the spatial congruence of ecosystems providing globally high levels of nature’s contributions to people, biodiversity, and areas with high development potential across several sectors. We find that conserving 44% of global land area through protection or sustainable management could provide 90% of current levels of ten of nature’s contributions to people and meet minimum representation targets for 26,709 terrestrial vertebrate species. This finding supports recent commitments by national governments under the Global Framework for Biodiversity to conserve at least 30% of global lands and waters. More than one-third of areas required for conserving nature’s contributions to people and species are also highly suitable for agriculture, renewable energy, oil and gas, mining, or urban expansion. This indicates potential conflicts among conservation, climate and development goals.
A Test for Evaluating Performance in Human-AI Systems
Authors: Malone Thomas , Vaccaro Michelle , Campero Andres , Song Jaeyoon , Wen Haoran , Almaatouq Abdullah 
Published: April 2023

Abstract

Many important uses of AI involve augmenting humans, not replacing them. But there is not yet a widely used and broadly comparable test for evaluating the performance of these human-AI systems relative to humans alone, AI alone, or other baselines. Here we describe such a test and demonstrate its use in three ways. First, in an analysis of 79 recently published results, we find that, surprisingly, the median performance improvement ratio corresponds to no improvement at all, and the maximum improvement is only 36%. Second, we experimentally find a 27% performance improvement when 100 human programmers develop software using GPT-3, a modern, generative AI system. Finally, we find that 50 human non-programmers using GPT-3 perform the task about as well as –- and less expensively than –- the human programmers. Since neither the non-programmers nor the computer could perform the task alone, this illustrates a strong form of human-AI synergy.
TREM-1 Aggravates Diabetic Associated Cognitive Impairment by Inducing Iron Deposition in Microglia via ERS
Authors: Zhao Yujing , Guo Hongyan , Li Qiao , Wang Nan , Yan Chaoying , Li Qing , Wang Qiang 
Published: April 2023

AbstractBackgroundCognitive impairment is one of the serious complications in diabetic patients. Iron accumulation is thought to be related to degenerative diseases and diabetes. Microglia have been shown to have features of iron accumulation in Alzheimer 's disease (AD). Triggering receptor expressed on myeloid cells-1(TREM-1)acts as an activating receptor for myeloid cells and is elevated in several neurodegenerative diseases. It is unclear whether microglial iron overload is involved in diabetic associated cognitive impairment (DACI), and whether there is an association between TREM-1 and iron metabolism.MethodsWe established a model cultured in high glucose (HG) for 72 hours in BV2/HMC3 and another one high fat diet (HFD) combined with STZ in C57 mice. Intracellular mitochondrial changes were observed by Transmission Electron Microscopy, intracellular Fe2 +, GSH/GSSG, MDA and ROS were detected using kits to assess lipid peroxidation in microglia. Prussian blue staining was used to observe iron deposition in the hippocampus. Cognitive performance of mice was assessed by Y-maze and novel object experiments (NOR). Western blot and immunofluorescence were used to observe the expression of iron and antioxidant-related protein (FPN1, FTL, TFR1,GPX4), apoptosis-related protein (BCL-2, BAX and Caspase3), TREM-1, endoplasmic reticulum stress (ERS)-related protein (BIP, P-IRE, IRE, ATF6, P-PERK, PERK, P-eIF2α, eIF2α, ATF4, CHOP).ResultsWe found that hippocampus and microglia undergo iron overload and antioxidant inactivation in HFD/STZ mice. Iron overload, with increase of TREM-1 and antioxidant inactivation, occurred in BV2/HMC3 cultured by HG. Fer-1 could alleviate it by inhibiting HG-induced change of FPN1, GPX4, TFR1, as well as Fe2 +, GSH/GSSG ratio, MDA and ROS. Inhibiting TREM-1 by LP17 could block it, too. Furthermore, PERK/ eIF2α/ATF4/CHOP was obviously down-regulated by LP17 in HG cultured BV2. When LP17 was administered intraperitoneally, cognitive impairment was improved in HFD/STZ mice, iron deposition and antioxidant inactivation in microglia of hippocampus were relieved.ConclusionsIn this study, we found that iron deposition and antioxidant inactivation occurred in microglia of hippocampus in HFD/STZ mice, accompanied by increase of TREM-1, while inhibition of TREM-1 expression alleviated it and improved cognitive dysfunction, which was partially regulated by PERK/ eIF2α/ATF4/CHOP.
Accelerating Atmospheric Gravity Wave Simulations using Machine Learning: Kelvin-Helmholtz Instability and Mountain Wave Sources Driving Gravity Wave Breaking and Secondary Gravity Wave Generation
Authors: DONG Wenjun , Fritts David , Lund Thomas , Liu Alan , Liu Hanli , Snively Jonathan 
Published: April 2023

Abstract

Gravity waves (GWs) and their associated multi-scale dynamics are known to play fundamental roles in energy and momentum transport and deposition processes throughout the atmosphere. We describe an initial, two-dimensional (2-D), machine learning model – the Compressible Atmosphere Model Network (CAMNet) - intended as a first step toward a more general, three-dimensional, highly-efficient, model for applications to nonlinear GW dynamics description. CAMNet employs a physics-informed neural operator to dramatically accelerate GW and secondary GW (SGW) simulations applied to two GW sources to date. CAMNet is trained on high-resolution simulations by the state-of-the-art model Complex Geometry Compressible Atmosphere Model (CGCAM). Two initial applications to a Kelvin-Helmholtz instability source and mountain wave generation, propagation, breaking, and SGW generation in two wind environments are described here. Results show that CAMNet can capture the key 2-D dynamics modeled by CGCAM with high precision. Spectral characteristics of primary and SGWs estimated by CAMNet agree well with those from CGCAM. Our results show that CAMNet can achieve a several order-of-magnitude acceleration relative to CGCAM without sacrificing accuracy and suggests a potential for machine learning to enable efficient and accurate descriptions of primary and secondary GWs in global atmospheric models.
Single-step genome-wide association studies and post-GWAS analyses for the number of oocytes and embryos in Gir cattle
Authors: Rocha Renata de Fátima Bretanha , Garcia Arielly Oliveira , Otto Pamela Itajara , Santos Mateus Guimarães dos , Silva Marcos Vinícius Gualberto Barbosa da , Martins Marta Fonseca , Machado Marco Antônio , Panetto João Claudio do Carmo , Guimarães Simone Eliza Facioni 
Published: April 2023

Abstract
Genome-Wide Association Studies (GWAS) are used for identification of quantitate trait loci (QTL) and genes associated with several traits. We aimed to identify QTLs, genes, and biological processes associated with number of total and viable oocytes, and number of embryos in Gir dairy cattle. A dataset with 17,526 follicular aspirations, including the following traits: number of viable oocytes (VO), number of total oocytes (TO) and number of embryos (EMBR) from 1,641 Gir donors was provided by five different stock farms. A genotype file with 2,093 animals and 395,524 SNP markers was used to perform a single-step GWAS analysis for each trait. The top 10 windows with the highest percentage of additive genetic variance explained by 100 adjacent SNPs were selected. QTLs were identified on chromosomes 1, 2, 5, 6, 7, 8, 9, 13, 17, 18, 20, 21, 22, 24 and 29. These QTLs were classified as External, Health, Meat and carcass, Production or Reproduction traits, and about 38% were related to Reproduction. In total, 117 genes were identified, of which 111 were protein-coding genes. Exclusively associations were observed for 42 genes with EMBR, and 1 with TO. Also, 42 genes were in common between VO and TO, 28 between VO and EMBR and four genes were in common among all traits. In conclusion, great part of the identified genes plays a functional role in initial embryo development or general cell functions. ARNT, EGR1, HIF1A, AHR and PAX2 are good markers for the production of oocytes and embryos in Gir cattle.
Rapid quantitation of trace perfluoroalkyl acids in soil by chelating resin-aided extraction and liquid chromatography-mass spectrometry analysis
Authors: Li Chenghua , Wang Yan , Liu Jinsong , Huang Guoliang , Zhang Baoshan , Jiang Kezhi 
Published: April 2023

Abstract
Perfluoroalkyl acids (PFAAs) are widely distributed persistent organic pollutants and their monitoring in environmental media is of wide public concern. Soil matrices are extremely complex, and the efficient and simple extraction of PFAAs from soil remains a challenge for analysts. In this work, we developed a simple and rapid method for the determination of 21 PFAAs in soil using chelating resin assisted extraction combined with LC-MS analysis. The addition of chelating resins was found to be used to remove free heavy metal ions from soil, thereby releasing PFAAs.Treatment with chelating resin greatly improved the extraction efficiency of PFAAs from soil, with the whole extraction process taking only 30 minutes. Under the optimized experimental conditions, the limits of quantification of the 21 PFAAs were in the range of 0.10–1.63 ng/g. Single PFAAs were detected in soil samples at concentrations between 0.10–2.60 ng/g and recovery experiments showed recoveries in the range of 70–126%.
Co-production within integrated care: a study protocol for multi-case study using Participatory Action Research within an Integrated Care System in England
Authors: Conquer Susan 
Published: April 2023

Abstract

Background
Globally, integrated health and care services are encouraged to work in collaboration with people who draw on their lived experience of health and care; co-producing change. Integrated Care Systems in England are recent structures, mandated in 2022, required to involve their service users, carers and citizens in strategic planning, service development, implementation and improvement. This multi-case study will use participatory action research to explore the impact of co-production on the design and transformation of services within integrated care.
Methods
Case studies of different examples of ongoing co-production within one Integrated Care System will be conducted simultaneously. Participatory action research will allow the researcher to partner with the participants as co-researchers, frame the research questions, and tailor the mixed methods. Co-researcher groups within each case study will consist of service leads, co-production project leads, service users, unpaid family carers, members of staff, and the researcher. Group meeting transcripts, co-researcher reflections, and other case study data collected will be continuously analysed and compared, developing a multi-case analysis.
Discussion
The knowledge built in each case will allow for interpretations of the data. The findings will contribute to the development of co-produced guidance for Integrated Care Systems. The co-researchers may be enabled to use the knowledge built during the case study as learning for their practice of co-production. The multi-case study findings will be submitted to a peer-reviewed international journal, and for conference presentation.
Discovery of inorganic glass electrolytes with polymer-like viscoelasticity
Authors: Hu Yong-Sheng , Dai Tao , Wu Siyuan , Lu Yaxiang , Yang Yang , Liu Yuan , Chang Chao , Rong Xiaohui , Xiao Rui-Juan , Zhao Junmei , Liu Yanhui , WANG Wei-Hua , Chen Liquan 
Published: April 2023

Abstract
Solid-state batteries offering both high energy density and safety have aroused widespread interest as promising power sources for electric vehicles. However, the interfacial mechanical stability of inorganic electrolyte is inferior to that of organic electrolytes and the high stack pressure (several to hundreds of megapascals) is required to maintain the intimate contact with electrodes. Here we report a class of inorganic glass solid electrolytes with polymer-like viscoelasticity, which possess both advantages of inorganic and polymer electrolytes and can enable pressure-less Li- and Na-based solid-state batteries (< 0.1 MPa). These electrolytes are synthesized by simply replacing chlorine of tetrachloroaluminates with oxygen, demonstrating high ionic conductivity of ~1 mS cm-1 at 30℃ for both Li+ and Na+. They can also exhibit superior chemo-mechanical compatibility with 4.3 V cathodes without additional stack pressure. Moreover, the inorganic glass solid electrolytes are feasible for scale-up, not only enabling to be made into thin films through a rolling process owing to its polymer-like flexibility but also facilitating the complete infiltration of the electrode materials like a liquid battery due to the low melting temperature below 160℃. We believe that these viscoelastic inorganic solid electrolytes will inspire us to design new solid electrolytes and accelerate practical application of pressure-less solid-state batteries.
A limit equilibrium method for the limiting landslide pressure acting on a retaining structure
Authors: Liu Shiyi , Li Ming 
Published: April 2023

Abstract
A novel limit equilibrium method is proposed for calculating the limiting landslide force acting on a planar sliding layer and on a retaining structure. The limiting landslide force can be determined by the horizontal force balance equation of the rigid block in the limit state adjacent to the retaining structure. Comparisons of the results obtained with the proposed method with the results obtained with the finite element method and limit analysis show that although the landslide pressure on one side of the rigid block is determined by the approximate method of curve fitting, the proposed method can be used in the design of landslide prevention. The proposed method can also analyse the influence of the soil-wall friction and the strength of the weak layer on the limiting landslide force. In addition, a simple, approximate, logarithmic spiral passive earth pressure theory-based formula is proposed to estimate the limiting landslide pressure for practical application.
Strain improvement for enhanced erythritol production by Moniliella pollinis Mutant-58 using jaggery as a cost-effective substrate
Authors: Khatape Anil B. , Rangaswamy Vidhya , Dastager Syed G. 
Published: April 2023

Abstract
Erythritol has been produced by various microorganisms including Yarrowia, Moniliella, Aureobasidium, and Candida strains. Due to its relatively high price erythritol sweetener used lesser than other polyols despite having many advantages. Therefore, in this study, Moniliella pollinis strain was improved for erythritol production by chemical mutagenesis and subsequently screening for cost-effective carbon sources for the enhanced erythritol yield. M. pollinis was subjected to N-methyl N-nitro N-nitroso guanidine (NTG), Ethyl methyl sulphonate (EMS), and UV mutagenesis for improved erythritol production. The mutant strains were evaluated for enhanced erythritol production medium optimization by using different carbon substrates at the shake flask level. To enhance the production of erythritol and statistical media optimization was carried out using a central composite design (CCD). Among 198 isolated mutants, Mutant-58 strain generated by EMS mutagenesis was selected for further assessment. The Mutant-58 strain showed significant morphological changes as compared to the parent strain. Furthermore, statistically optimized media composition resulted in the higher production of erythritol (91.2±3.4 g/L) with a yield of 40.7±3.4 % in shake flask experiments. The optimized medium composition for erythritol production constitutes (g/L) 225 jaggery, 4.4 yeast extract (YE), 4.4 KH2PO4, 0.31 MgSO4, and pH 5.5. The present study demonstrated strain improvement, media, and process optimization resulting in a 30% increase in the erythritol production in the Mutant-58 as compared to the parent strain. This is also the first instance where jaggery has been used as a cost-effective carbon source alternative to glucose for industrial-scale erythritol production.
INDIRECT: Invertible and Discrete Noisy Image Rescaling with Enhancement from Case-dependent Textures
Authors: Chen Yan-An , Hsiao Ching-Chun , Peng Wen-Hsiao , Huang Ching-Chun 
Published: April 2023

Abstract
Rescaling digital photos to display them on heterogeneous devices while removing the noise has gradually gained attention. However, little research focused on a unified framework to perform these tasks jointly and efficiently. We propose a novel method, INDIRECT (INvertible and Discrete noisy Image Rescaling with Enhancement from Case-dependent Textures), to simultaneously address image denoising and rescaling. With a jointly optimized framework, INDIRECT can produce clean and visually pleasing images with a lightweight model. Specifically, INDIRECT first introduces a discrete invertible network, DDR-Net, to perform rescaling and denoising through its reversible operations. Its discrete nature efficiently alleviates the quantization error occurring during downscaling. Then, a case-dependent texture module (CTM) is proposed to estimate the missing high-frequency information and recover a clean and high-resolution image. Experimental results show our method achieves competitive performance on three tasks–the noisy image rescaling, the image rescaling, and the denoising tasks–with a comparatively small model.
Magnetic Field and Plasma Diagnostics for Solar Coronal Mass Ejections: A Case Study Using the Forward Modeling Approach
Authors: Liu Xianyu , Tian Hui , Torok Tibor , Gibson Sarah , Yang Zihao , Li Wenxian , Samanta Tanmoy 
Published: April 2023

Abstract
The proposed COronal Solar Magnetism Observatory (COSMO) Large Coronagraph (LC) will provide unique observations to study coronal mass ejections (CMEs) with its ability to diagnose the magnetic field and plasma properties in the solar corona. Here we take a realistic magnetohydrodynamic CME model, and synthesize the signals of several coronal emission lines (CELs) to perform forward modeling of COSMO LC observation of a CME. We use the Stokes parameters of the Fe xiii 10747 ̊A line to diagnose the magnetic field and plasma properties of the CME flux rope. The results show that COSMO LC can provide magnetic field measurements of CME progenitors with a high spatial resolution (pixel size = 2′′). During the CME eruption, the COSMO LC observation may be used to qualitatively study the evolution of magnetic field by using a lower spatial resolution (pixel size = 6′′). We then use the synthetic signals of several other CELs to diagnose the physical conditions in the CME leading front, including the shock. The COSMO LC observations of the Fe xiii 10798/10747 ̊A and Ar xiii 8300/10143 ̊A line pair could provide density diagnostics of the front. By observing several CELs with different formation temperatures, the COSMO LC could be used to diagnose the temperature and ionization states in the front. We suggest that the Fe xiii 10747 ̊A line should be given the highest priority when observing CMEs, while observations of the Fe xiii 10798 ̊A, Fe xiv 5303 ̊A, Fe xv 7062 ̊A, and Ar xiii 10143 ̊A lines can also provide valuable information on CMEs.