bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parallel sequencing of extrachromosomal circular DNAs and transcriptomes in single cancer cells
Authors: Chamorro González Rocío , Conrad Thomas , Stöber Maja C. , Xu Robin , Giurgiu Mădălina , Rodriguez-Fos Elias , Kasack Katharina , Brückner Lotte , van Leen Eric , Helmsauer Konstantin , Dorado Garcia Heathcliff , Stefanova Maria E. , Hung King L. , Bei Yi , Schmelz Karin , Lodrini Marco , Mundlos Stefan , Chang Howard Y. , Deubzer Hedwig E. , Sauer Sascha , Eggert Angelika , Schulte Johannes H. , Schwarz Roland F. , Haase Kerstin , Koche Richard P. , Henssen Anton G. 
Published: May 2023

AbstractExtrachromosomal DNAs (ecDNAs) are common in cancer, but many questions about their origin, structural dynamics and impact on intratumor heterogeneity are still unresolved. Here we describe single-cell extrachromosomal circular DNA and transcriptome sequencing (scEC&T-seq), a method for parallel sequencing of circular DNAs and full-length mRNA from single cells. By applying scEC&T-seq to cancer cells, we describe intercellular differences in ecDNA content while investigating their structural heterogeneity and transcriptional impact. Oncogene-containing ecDNAs were clonally present in cancer cells and drove intercellular oncogene expression differences. In contrast, other small circular DNAs were exclusive to individual cells, indicating differences in their selection and propagation. Intercellular differences in ecDNA structure pointed to circular recombination as a mechanism of ecDNA evolution. These results demonstrate scEC&T-seq as an approach to systematically characterize both small and large circular DNA in cancer cells, which will facilitate the analysis of these DNA elements in cancer and beyond.
A high-quality chromosomal-level genome assembly of Greater Scaup (Aythya marila)
Authors: Zhou Shengyang , Xia Tian , Gao Xiaodong , Lyu Tianshu , Wang Lidong , Wang Xibao , Shi Lupeng , Dong Yuehuan , Zhang Honghai 
Published: May 2023

AbstractAythya marila is one of the few species of Anatidae, and the only Aythya to live in the circumpolar. However, there is a relative lack of research on genetics of this species. In this study, we reported and assembled the first high-quality chromosome-level genome assembly of A. marila. This genome was assembled using Nanopore long reads, and errors corrected using Illumina short reads, with a final genome size of 1.14 Gb, scaffold N50 of 85.44 Mb, and contig N50 of 32.46 Mb. 106 contigs were clustered and ordered onto 35 chromosomes based on Hi-C data, covering approximately 98.28% of the genome. BUSCO assessment showed that 97.0% of the highly conserved genes in aves_odb10 were present intact in the genome assembly. In addition, a total of 154.94 Mb of repetitive sequences were identified. 15,953 protein-coding genes were predicted in the genome, and 98.96% of genes were functionally annotated. This genome will be a valuable resource for future genetic diversity and genomics studies of A. marila.
Integrated gene expression profiles reveal a transcriptomic network underlying the thermogenic response in adipose tissue
Authors: Rodó Jordi , Garcia Miquel , Casana Estefania , Muñoz Sergio , Jambrina Claudia , Sacristan Victor , Franckhauser Sylvie , Grass Ignasi , Jimenez Veronica , Bosch Fatima 
Published: May 2023

AbstractObesity and type 2 diabetes are two closely related diseases representing a serious threat worldwide. An increase in metabolic rate through enhancement of non-shivering thermogenesis in adipose tissue may represent a potential therapeutic strategy. Nevertheless, a better understanding of thermogenesis transcriptional regulation is needed to allow the development of new effective treatments. Here, we aimed to characterize the specific transcriptomic response of white and brown adipose tissues after thermogenic induction. Using cold exposure to induce thermogenesis in mice, we identified mRNAs and miRNAs that were differentially expressed in several adipose depots. In addition, integration of transcriptomic data in regulatory networks of miRNAs and transcription factors allowed the identification of key nodes likely controlling metabolism and immune response. Moreover, we identified the putative role of the transcription factor PU.1 in the regulation of PPARγ-mediated thermogenic response of subcutaneous white adipose tissue. Therefore, the present study provides new insights into the molecular mechanisms that regulate non-shivering thermogenesis.
Study of the disintegration of loess modified with fly ash and Roadyes
Authors: Li Hongru , Yang Min , Guo Xiaohan 
Published: May 2023

AbstractThe disintegration property of loess is the wetting and subsequent disintegration of loess in water, which is generally an important index for resistance to erosion and disintegration of wet loess slopes and foundations. In this study, a disintegration instrument is developed in this laboratory and used to study the disintegration properties of fly ash-modified loess in foundations and Roadyes-modified loess in subgrades. Disintegration tests are used to compare samples of loess modified with different amounts of fly ash and Roadyes, different water contents and different dry densities; the influence of fly ash and Roadyes content on the disintegration of modified loess is analyzed. The differences in disintegration properties between the pure loess and modified loess are compared to explore the evolution of disintegration properties of modified loess and the optimal incorporation levels of fly ash and Roadyes. The experimental results show that the incorporation of fly ash reduces the disintegration of loess, while the incorporation of Roadyes likewise decreases the disintegration of loess. The disintegration of the loess modified with the two curing agents is better than that of the pure loess and loess mixed with a single curing agent; the optimal incorporation levels are 15% fly ash and 0.5‰ Roadyes. Comparing the evolution of the disintegration curves of samples of loess with different modifications shows is a linear relationship between time and amount of disintegration for pure loess and Roadyes-modified loess. Thus, a linear disintegration model is established in which the parameter P is the disintegration rate. According to the exponential relationship between time and amount of disintegration of fly ash-modified loess and loess modified with both fly ash and Roadyes, an exponential disintegration model is established in which the water stability parameter Q affects the strong and weak disintegration of the modified loess. The relationship between the water stability of the loess (modified with added fly ash and Roadyes) in water and the initial water content and dry density is analyzed. The water stability of the loess first increases and then decreases with increasing initial water content and gradually increases with increasing dry density. When the sample density is the maximum dry density, the sample has the best water stability. These research results provide a basis for the application of loess modified with added fly ash and Roadyes.
Sediment resuspension due to internal solitary waves of elevation in the Messina Strait (Mediterranean Sea)
Authors: La Forgia Giovanni , Droghei Riccardo , Pierdomenico Martina , Falco Pierpaolo , Martorelli Eleonora , Bergamasco Alessandro , Bergamasco Andrea , Falcini Federico 
Published: May 2023

AbstractBy combining real-field observations and theoretical predictions, we describe role and relationships among north-propagating internal solitary waves (ISWs) generated by tidal currents in the Messina Strait (Mediterranean Sea), buoyancy deformation, sediment resuspension, and mixing effects. In particular, our results show that the presence of ISWs traveling along the Gioia Basin (north of the Strait) is not strictly related to seasonality. During winter, when the remote observation of ISWs from satellite is particularly rare due to the weak water column stratification, we observe elevation-type ISWs from hydrographic data. This finding reveals a different scenario with respect to the summer one, when the high stratified water column gives rise to depression-type north-propagating ISWs and the subsequent sea surface manifestations, detectable from satellite imagery. Moreover, our beam transmission observations and theoretical predictions of the induced near-bottom horizontal velocity suggest that these elevation-type ISWs induce sediment resuspension over the seafloor, as well as mixing effects as they break on the frontal slope nearby Capo Vaticano.
Relationship between reactive group chemistry and printing properties of heterofunctional reactive dyes via screen printing
Authors: Siddiqua Umme Habibah , Ali Shaukat , Tufail Aasma , Gatasheh Mansour K. , Riaz Luqman , Yasir Muhammad Wahab 
Published: May 2023

AbstractScreen printing of cotton fabric using newly synthesized azo reactive dyes was carried out in the present study. Functional group chemistry and its effect on the printing properties of cotton fabric by varying the nature, number and position of reactive groups of synthesized azo reactive dyes (D1–D6) was studied. Different printing parameters (Temperature, alkali and urea) and their effect was explored on the physicochemical printing properties e.g., fixation, color yield, and penetration of the dyed cotton fabric. Data revealed that dyes with more reactive groups and having linear and planar structures (D-6) showed enhanced printing properties. Spectraflash spectrophotometer was used to evaluate the colorimetric properties of screen-printed cotton fabric and results showed superb color buildup. Printed cotton samples displayed excellent to very good ultraviolet protection factor (UPF). Presence of sulphonate groups and excellent fastness properties may entitle these reactive dyes as commercially viable for urea free printing of cotton fabric.
Validation of immunoassays for the Chlamydia trachomatis antigen Pgp3 using a chimeric monoclonal antibody
Authors: Goodhew Brook , Tang Xiaoling , Goldstein Jason , Lee Joo , Martin Diana , Gwyn Sarah 
Published: May 2023

AbstractSeroepidemiology, or measuring antibodies to pathogens to estimate population-level exposure, can provide useful public health data. The tests used, however, often lack sufficient validation data due to absence of a gold standard. For many pathogens, serum antibodies can be detected long after resolution of infection, but infection status is often used as a gold standard for antibody positivity. To ensure that recently developed antibody tests for seroepidemiology of Chlamydia trachomatis (Ct), the causative agent of urogenital chlamydia and the blinding eye disease trachoma, have high performance, we generated a chimeric antibody to the immunodominant Ct antigen Pgp3. Two clones were selected to evaluate the test performance of three assays to measure antibodies to Pgp3: multiplex bead assay (MBA), enzyme-linked immunosorbent assay (ELISA), and lateral flow assay (LFA). Overall, each assay demonstrated high accuracy and precision when tested using either clone, and the clones were stable when stored at − 20 °C and 4 °C for almost 2 years. The limit of detection was similar for MBA and LFA, but almost a log-fold higher (i.e. less sensitive) using ELISA. Overall, the chimeric antibodies represent stable control reagents for tests with robust performance and will facilitate deployment of these tests to other laboratories.
Investigating the effects of wind loading on three dimensional tree models using numerical simulation with implications for urban design
Authors: Amani-Beni Majid , Tabatabaei Malazi Mahdi , Dehghanian Kaveh , Dehghanifarsani Laleh 
Published: May 2023

AbstractIn this study, the effects of wind on an Eastern Red Cedar were investigated using numerical simulations. Two different tree models were proposed, each with varying bole lengths and canopy diameters. A total of 18 cases were examined, including different canopy diameters, bole lengths, and wind velocities. Using computational fluid dynamics (CFD) methods, the drag force, deformation, and stress of the tree models were calculated under different wind velocities and geometric parameters. A one-way fluid–structure interaction (FSI) method was used to solve the deformation of the tree. Additionally, velocity and pressure distribution around the tree were obtained. The results indicate that wind velocity and geometric parameters of the tree have a significant impact on deformation, drag force, and stress. As wind velocity increases from 15 to 25 m/s, the force on the tree increases substantially. The results also show that the diameter of the canopy has a bigger effect on stress and strain than the bole length. This study provides insights into tree behavior under wind loading for urban planning and design, informing optimal tree selection and placement for windbreak effectiveness and comfortable environments.
Fishery resource management with migratory prey harvesting in two zones- delay and stochastic approach
Authors: Niranjan H. , Srinivas M. N. , Murty A. V. S. N. , Viswanathan K. K. 
Published: May 2023

AbstractIn this work, we looked at a two-zone aquatic habitat where both prey and predators can access the zones. The prey alternates between two zones at random. The growth of prey in the absence of a predator is believed to be logistic in each zone. The inner steady state is determined. Around the interior steady state, the deterministic model’s local and global stability is investigated. Furthermore, a stochastic stability study is performed in the neighbourhood of a positive steady state, using analytical estimates of population mean square fluctuations to investigate the system’s dynamics in the presence of Gaussian white noise.
Design theory of compact power divider with reconfigurable power division and negative group delay characteristics
Authors: Nair Rekha G. , S Natarajamani 
Published: May 2023

AbstractThis article presents the combined analysis of reconfigurable power division and negative group delay (NGD) in a power divider. A novel composite transmission line based reconfigurable power divider with high power division ratio, variable negative group delay, and lower characteristic impedance is presented in this work. The impedance transformation in composite transmission lines control both negative group delay and power division. This power divider possesses a wide range of power division ratios from 1 to 39, adequate isolation, impedance matching, and NGD of $$-3.4$$

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3.4

ns to $$-4.7$$

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4.7

ns in the reconfigurable transmission path. The negative group delay is achieved without using any additional group delay circuits. Theoretical equations corresponding to the low characteristic impedance of the transmission line sections and that of isolation elements are derived. The measurement results justify the attainment of high tuning of the power division ratio and negative group delay. Isolation and return loss are higher than − 15 dB at the centre frequency of 1.5 GHz. The significant contributions of this design can be listed as the wide reconfigurable power division along with negative group delay and reduced size.
l-Lactate treatment by photosynthetic cyanobacteria expressing heterogeneous l-lactate dehydrogenase
Authors: Kato Yuichi , Inabe Kosuke , Haraguchi Yuji , Shimizu Tatsuya , Kondo Akihiko , Hasunuma Tomohisa 
Published: May 2023

Abstractl-Lactate is a major waste compound in cultured animal cells. To develop a sustainable animal cell culture system, we aimed to study the consumption of l-lactate using a photosynthetic microorganism. As genes involved in l-lactate utilization were not found in most cyanobacteria and microalgae, we introduced the NAD-independent l-lactate dehydrogenase gene from Escherichia coli (lldD) into Synechococcus sp. PCC 7002. The lldD-expressing strain consumed l-lactate added to basal medium. This consumption was accelerated by expression of a lactate permease gene from E. coli (lldP) and an increase in culture temperature. Intracellular levels of acetyl-CoA, citrate, 2-oxoglutarate, succinate, and malate, and extracellular levels of 2-oxoglutarate, succinate, and malate, increased during l-lactate utilization, suggesting that the metabolic flux from l-lactate was distributed toward the tricarboxylic acid cycle. This study provides a perspective on l-lactate treatment by photosynthetic microorganisms, which would increase the feasibility of animal cell culture industries.
2-Oxoglutarate contributes to the effect of foliar nitrogen on enhancing drought tolerance during flowering and grain yield of soybean
Authors: Gai Zhijia , Zhang Maoming , Zhang Pengfei , Zhang Jingtao , Liu Jingqi , Cai Lijun , Yang Xu , Zhang Na , Yan Zhengnan , Liu Lei , Feng Guozhong 
Published: May 2023

AbstractDrought severely affects the growth and yield of soybean plants especially during the flowering period. To investigate the effect of 2-oxoglutarate (2OG) in combination with foliar nitrogen (N) at flowering stage on drought resistance and seed yield of soybean under drought stress. This experiment was conducted in 2021 and 2022 on drought-resistant variety (Hefeng 50) and drought-sensitive variety (Hefeng 43) soybean plants treated with foliar N (DS + N) and 2-oxoglutarate (DS + 2OG) at flowering stage under drought stress. The results showed that drought stress at flowering stage significantly increased leaf malonaldehyde (MDA) content and reduced soybean yield per plant. However, superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) activities were significantly increased by foliar N treatment, and 2-oxoglutarate synergistically with foliar N treatment (DS + N + 2OG) was more beneficial to plant photosynthesis. 2-oxoglutarate significantly enhanced plant N content, glutamine synthetase (GS) and glutamate synthase (GOGAT) activity. Furthermore, 2-oxoglutarate increased the accumulation of proline and soluble sugars under drought stress. Under drought stress, soybean seed yield was increased by DS + N + 2OG treatment by 16.48–17.10% and 14.96–18.84% in 2021 and 2022, respectively. Thus, the combination of foliar N and 2-oxoglutarate better mitigated the adverse effects of drought stress and could better compensate for the yield loss of soybean under drought stress.
A clinical study of the correlation between metabolic-associated fatty liver disease and coronary plaque pattern
Authors: Zhang Zhijiao , Zheng Mengyao , Lei Hongtao , Jiang Zimeng , Chen Yuhang , He Haiyu , Zhao Gongfang , Huang Hua 
Published: May 2023

AbstractNonalcoholic fatty liver disease (NAFLD) is the hepatic manifestation of metabolic syndrome (MetS) and has been correlated with coronary atherosclerosis (CAS). Since NAFLD was renamed metabolic-associated fatty liver disease(MAFLD) in 2020, no studies have evaluated the correlation between MAFLD and CAS. The aim of this study was to evaluate the relationship between MAFLD and CAS. A total of 1330 patients underwent continuous coronary computed tomography angiography (CCTA) and abdominal ultrasound as part of a routine physical examination. Ultrasonography was used to assess fatty liver, and CCTA was used to assess coronary artery plaques, degree of stenosis, and diseased blood vessels. Univariate and multivariate logistic regression analyses were performed with plaque type and degree of stenosis as dependent variables and MAFLD and traditional cardiovascular risk factors as independent variables to analyze the correlation between MAFLD and CAS. Among the 1164 patients, 680 (58.4%) were diagnosed with MAFLD through a combination of ultrasound and auxiliary examinations. Compared with the non-MAFLD group, the MAFLD group had more cardiovascular risk factors,and the MAFLD group had more likely to have coronary atherosclerosis, coronary stenosis and multiple coronary artery stenosis.In the univariate logistic regression, MAFLD was significantly correlated with overall plaque, calcified plaques, noncalcified plaques, mixed plaques,and significant stenosis in the coronary arteries.(p < 0.05). After adjusting for cardiovascular risk factors , MAFLD was correlated with noncalcified plaques (1.67; 95% confidence interval (CI) 1.15–2.43; p = 0.007) and mixed plaques (1.54; 95% CI 1.10–2.16; p = 0.011). In this study, MAFLD group had more cardiovascular risk factors, MAFLD was correlated with coronary atherosclerosis,and significant stenosis.Further study found independent associations between MAFLD and noncalcified plaques and mixed plaques, which suggest a clinically relevant link between MAFLD and coronary atherosclerosis.
Infection of neonatal mice with the murine norovirus strain WU23 is a robust model to study norovirus pathogenesis
Authors: Peiper Amy M. , Helm Emily W. , Nguyen Quyen , Phillips Matthew , Williams Caroline G. , Shah Dhairya , Tatum Sarah , Iyer Neha , Grodzki Marco , Eurell Laura B. , Nasir Aqsa , Baldridge Megan T. , Karst Stephanie M. 
Published: May 2023

AbstractNoroviruses are the leading cause of severe childhood diarrhea and foodborne disease worldwide. While they are a major cause of disease in all age groups, infections in the very young can be quite severe, with annual estimates of 50,000–200,000 fatalities in children under 5 years old. In spite of the remarkable disease burden associated with norovirus infections, very little is known about the pathogenic mechanisms underlying norovirus diarrhea, principally because of the lack of tractable small animal models. The development of the murine norovirus (MNV) model nearly two decades ago has facilitated progress in understanding host–norovirus interactions and norovirus strain variability. However, MNV strains tested thus far either do not cause intestinal disease or were isolated from extraintestinal tissue, raising concerns about translatability of research findings to human norovirus disease. Consequently, the field lacks a strong model of norovirus gastroenteritis. Here we provide a comprehensive characterization of a new small animal model system for the norovirus field that overcomes prior weaknesses. Specifically, we demonstrate that the WU23 MNV strain isolated from a mouse naturally presenting with diarrhea causes a transient reduction in weight gain and acute self-resolving diarrhea in neonatal mice of several inbred mouse lines. Moreover, our findings reveal that norovirus-induced diarrhea is associated with infection of subepithelial cells in the small intestine and systemic spread. Finally, type I interferons (IFNs) are critical to protect hosts from norovirus-induced intestinal disease whereas type III IFNs exacerbate diarrhea. This latter finding is consistent with other emerging data implicating type III IFNs in the exacerbation of some viral diseases. This new model system should enable a detailed investigation of norovirus disease mechanisms.
The influence of genetic and acquired factors on the vulnerability to develop depression: a review
Authors: Zhang Xingfang , Qiao Yajun , Wang Mengyuan , Liang Xinxin , Zhang Ming , Li Cen , Cairang Jixian , Wang Jianv , Bi Hongtao , Gao Tingting 
Published: May 2023

Abstract
Depression is one of the most common mental disorders that affects hundreds of millions of people worldwide and has claimed tens of thousands of lives. The causes are divided into two main areas: congenital genetic factors and acquired environmental factors. Congenital factors include genetic mutations and epigenetic events; acquired factors include birth patterns, feeding patterns, dietary patterns, childhood experiences, education and economic levels, isolation due to epidemics, and many other complex factors. According to studies, these factors play important roles in depression. Therefore, here, we analyze and study the factors from two aspects, describe their influence on individual depression, and analyze their underlying mechanisms. The results showed that both innate and acquired factors have significant effects on the occurrence of depressive disorder, and these findings may provide new ideas and methods for the study of depressive disorder, thus facilitating the process of depression prevention and treatment.