bluuebunny/crossref_metadata_2025_split huggingface dataset:
A casein kinase TaCK2α contributes to wheat resistance to Puccinia triticina
Authors: Zhang Yanjun , Ma Qiuying , Geng Huaimin , Wang Shen , Cui Zhongchi , Wang Haiyan , Liu Daqun 
Published: February 2023

Abstract
Background The casein kinase 2 (CK2), one of the major multifunctional protein kinases in plant cells, is expressed ubiquitously and is essential for survival in response to different stresses. However, the role of CK2 in the interaction between wheat and Puccinia triticina (Pt) is still unknown.
Results Our earlier studies have found that one casein kinase CK2 named TaCK2α was screened from RNA-seq data in wheat line TcLr19 inoculated by Pt. In this study, quantitative real-time PCR (qPCR) analysis showed that TaCK2αexpression was induced by Pt race PHNT and signaling molecules, suggesting that it might play a role in the interaction of wheat-Pt associated with abscisic acid (ABA) and ethylene (ETH) signaling molecules. To further determine the function of the TaCK2αgene in wheat resistance to Pt, protein-mediated phenotyping assays in vivo and antifungal activity assays in vitrodemonstrated that wheat leaves infiltrated with pure TaCK2α protein developed significantly less disease compared to control leaves. Then virus-induced gene silencing (VIGS) system confirmed that TaCK2α was involved in regulating wheat resistance to Pt. In addition, 24 candidates with potential interacting with TaCK2α (2 disease resistance related protein, 11 stress resistance related protein, 1 photosynthesis related proteins, and 10 functional indeterminate protein) were selected in wheat by pull-down assay combination with mass spectrometry (MS). Conclusions Overall, our results indicate that TaCK2α gene mediated wheat resistance to Pt, laying a good foundation to analyze the molecular mechanisms of CK2 in plant resistance to biotic stress.
Complete genome analysis and biological characterization of a novel Clostridium perfringens phage vB_CP_qdyz_P5
Authors: Wang Yue , Zhao Gang , Wang Jingxue , Lin Hong 
Published: February 2023

Abstract
A novel lytic Clostridium perfringens phage, named vB_CP_qdyz_P5, was isolated and characterized in this study. Genome analysis revealed that vB_CP_qdyz_P5 has a linear double-stand DNA of 18888 bp with a G+C content of 28.8%. There were 27 opening reading frames in its genome. Moreover, vB_CP_qdyz_P5 showed good temperature (below 70℃) and pH (4 to 12) stabilities as well as a very strong lysis ability with a high burst size(207pfu/cell). Phylogenetic analysis indicated that vB_CP_qdyz_P5 might be a novel phage of the family Guelinviridae.
Chatbots and Robots: A framework for the self-management of occupational stress
Authors: Yorita Akihiro , Egerton Simon , Chan Carina , Flower Rebecca , Kubota Naoyuki 
Published: February 2023

Abstract
We have developed a stress management framework aimed at helping healthcare professionals manage occupational stress. A chatbot is used to gather pertinent information from a user through regular conversation which is processed via a fuzzy inference model to derive their level of occupational Comprehensibility, Manageability, Meaningful and overall occupational Sense of Coherence (SOC). This analysis feeds into a Peer Support model which selects the best intervention aimed at enhancing a user’s stress-coping abilities and reducing their levels of occupational stress. A trial has been conducted with working adults, and the results demonstrate that the approach is able to measure user stress and provide accurate analysis and relevant peer support.
The association between sex and neonatal respiratory distress syndrome
Authors: Fang Keren , Yue Shaojie , Wang Shuo , Wang Mingjie , Yu Xiaohe , Ding Ying , Lv Mei , Liu Yang , Cao Chuanding , Liao Zhengchang 
Published: February 2023

Abstract
Background: To investigate the association between sex and neonatal respiratory distress syndrome (NRDS).
Methods: Infants born at our hospital and transferred to the neonatal department within 1 hour were retrospectively analyzed. Depending on whether they developed NRDS during their hospital stay, the infants was divided into NRDS and non-NRDS groups. There were 142 infants in the NRDS group (95 males and 47 females) and 310 infants in the non-NRDS group (180 males and 140 females). The infants’ data on gestational age, sex, birth weight, white blood cell count (WBC), platelet count (PLT), C-reactive protein (CRP), immunoglobulin M (IgM), gestational diabetes mellitus(GD), antenatal steroids use, meconium-stained amniotic fluid, and preterm premature rupture of membranes(PPROM）were gathered.
Results: 452 infant (265 males and 187 females) were involved for the purpose of collecting basic characteristic. Multivariate analysis, males had a 1.87 times higher risk of NRDS than females (P<0.05) after controlling for the confounding effects of gestational age, birth weight, WBC, PLT, CRP, IgM, GD, antenatal steroids use, meconium-stained amniotic fluid, and PPROM.
Conclusions: Sex was associated with NRDS; males had a considerably higher risk of NRDS than females.
Therapeutic effect of V8 affecting mitophagy and endoplasmic reticulum stress in acute myeloid leukemia mediated by ROS and CHOP signaling
Authors: Hui Hui , Guo Yongjian , Zhu Mengyuan , Wang Zhanyu , Chen Hongyu , Qing Yingjie , Wang Hongzheng , Xu Jingyan , Li Hui 
Published: February 2023

AbstractAcute myeloid leukemia (AML) is a disease of malignant proliferation of abnormally or poorly differentiated myeloid cells of the hematopoietic system. The clinical treatments of non-M3 AML are experiencing a lack of effective drugs. V8 is a newly synthesized derivative of the natural flavonoid wogonin, which belongs to the potential anticancer drug, and has shown significant antitumor activityin vitroandin vivo. In this study, we investigated the effects of V8 on AML cell lines and primary AML cells and the underlying mechanisms. The results showed that V8 inhibited the growth and induced the apoptosis of AML cell lines (ME-1, Kasumi-1, and U937) and primary AML cells in a concentration-dependent manner. Meanwhile, we revealed that V8-induced apoptosis was accompanied by mitochondrial injury, such as the reduction of mitochondrial membrane potential and ATP production, activation of endoplasmic reticulum stress (ERS) characterized by GRP78 and caspase-12 expression upregulation. Mechanism studies have shown that V8 induced mitochondrial injury and inhibited mitophagy via elevating the intracellular ROS level. In addition, V8 activated PERK-p-eIF2α-ATF4 and Ire1α-XBP1 pathways and induced apoptosis of AML cells via selectively activating CHOP. Correspondingly, the degree of apoptosis and expression of apoptosis-related proteins were alleviated after the elimination of cytoplasmic ROS with N-Acetyl-L-cysteine (NAC) and knocking out CHOP in the cells by transfection with CHOP shRNA, implicating that mitochondrial injury-triggered upregulation of ROS and CHOP played an important role in V8-induced apoptosis of AML cells. In primary AML cells-bearingNOD/SCIDmice model and U937 cells-inoculatingBALB/cnude mice xenografts transplantation tumor model, administration of V8 markedly prolonged survival time and inhibited the xenografts growth via CHOP-mediated ERSin vivo. In conclusion, our study provides a new insight into the mechanism of V8-induced apoptosis, suggesting the potential of V8 as a promising agent against AML.
Vascularized patient-derived tumoroids supplemented with immune cells to predict response towards treatment for lung cancer patients
Authors: Lê Hélène , Ponté Charlotte , Desforges Jules , Hua Guoqiang , Idoux-Gillet Ysia , Lindner Véronique , Olland Anne , Falcoz Pierre-Emanuel , Zaupa Cécile , Quéméneur Eric , Balloul Jean-Marc , Jessel Nadia 
Published: February 2023

Abstract
We here describe a prototype of a patient-derived tumoroid that prefigures the precision medicine approach by helping experimental assessment of response to current treatments. The introduction of microvessels to help forming a tumor-connected vasculature, and of peripheral blood immune cells was shown to be essential for the representativeness of the model. The study is based on a cohort of 11 patients at various stages of the disease. Noteworthy, this predictive vascularized, and immunocompetent micromodel can be obtained within 2 weeks, matching the constraints of the patient journey. Histological analyses confirmed that major features of the original tumor were conserved. Transcriptomic analysis confirmed the functionality of the tumoroid. The responses to either anti-angiogenic treatment or platinum-based chemotherapy regimen highlighted the role of immune mechanisms. We also discussed the possibility to apply this original experimental model to the analysis of response to immune checkpoint blockers, or oncolytic vector-based therapies.
The contribution of multiplexing single cell RNA sequencing in acute myeloid leukemia
Authors: Madaci Lamia , Gard Charlyne , Nin Sébastien , Venton Geoffroy , Rihet Pascal , Puthier Denis , Loriod Béatrice , Costello Régis 
Published: February 2023

Abstract
After decades during which the treatment of acute myeloid leukemia consisted in cytarabine + anthracycline, targeted therapies have appeared, first based on monoclonal antibodies (anti-CD52, anti-CD123) and then on specific inhibitors of molecular mutations (anti-IDH, IDH2 or FLT3). What should be the place of these therapeutic options considering the tumor heterogeneity inherent to leukemia diagnosis and the clonal drift of which this type of tumor is capable? Targeted drugs would require an analysis of the various therapeutic targets not in the total population but at the individual cell level. Indeed, the prognostic value and therapeutic interest of a given molecular target are certainly not the same if it is a cell in terminal differentiation with low proliferative potential or, on the contrary, a stem cell with strong capacities of both proliferation and self-renewal. However, this cell-by-cell analysis is fraught with several pitfalls. The first one is scientific because the comparison of two different single cell analysis experiments is delicate, in spite of the different techniques aiming at standardizing the results. The second pitfall is practical, as each single cell experiment is very costly from a financial point of view but also very time consuming. The solution is therefore to be able to process several samples at the same time, which is the specificity of the cell hashing technique. In this study we demonstrate that the cell hashing technique can be used for the analysis of acute myeloid leukemia cells. We compared the cell hashing technique with the classic single cell analysis and demonstrated a good concordance of different parameters: quality control, gene expression correlation, expression analysis of leukemic blast markers in both patients. The technique could thus in the future be part of the biological assessment of acute myeloid leukemia and contribute to the individualization and optimization of their management, particularly in the context of the use of targeted therapies.
New statistical selection method for pleiotropic variants associated with both quantitative and qualitative traits
Authors: Kim Kipoong , Jun Tae-Hwan , Ha Bo-Keun , Wang Shuag , Sun Hokeun 
Published: February 2023

Abstract
Background Identification of pleiotropic variants associated with multiple phenotypic traits has received increasing attention in genetic association studies. Overlapping genetic associations from multiple traits help to detect weak genetic associations missed by single-trait analyses. Many statistical methods were developed to identify pleiotropic variants with most of them being limited to quantitative traits when pleiotropic effects on both quantitative and qualitative traits have been observed. This is a statistically challenging problem because there does not exist an appropriate multivariate distribution to model both quantitative and qualitative data together. Alternatively, meta-analysis methods can be applied, which basically integrate summary statistics of individual variants associated with either a quantitative or a qualitative trait without accounting for correlations among genetic variants.
Results We propose a new statistical selection method based on a unified selection score quantifying how a genetic variant, i.e., a pleiotropic variant associates with both quantitative and qualitative traits. In our extensive simulation studies where various types of pleiotropic effects on both quantitative and qualitative traits were considered, we demonstrated that the proposed method outperforms the existing meta-analysis methods in terms of true positive selection. We also applied the proposed method to a peanut dataset with 6 quantitative and 2 qualitative traits, and a cowpea dataset with 2 quantitative and 6 qualitative traits. We were able to detect some potentially pleiotropic variants missed by the existing methods in both analyses.
Conclusions The proposed method is able to locate pleiotropic variants associated with both quantitative and qualitative traits. It has been implemented into an R package `UNISS', which can be downloaded from http://github.com/statpng/uniss
Aerosol-induced effects on pre- and developed Indian summer monsoon and the corresponding onset and withdrawal
Authors: Huang Kuan-Tzu , Sui Chung-Hsiung , Lo Min-Hui , Kuo Yu-Yang , Chang Chiung-Wen June 
Published: February 2023

Abstract
The NCAR Community Earth System Model is used to study aerosol direct effect on Indian summer monsoon (ISM). We perform two sets of 30-year simulations subject to prescribed perpetual SST annual cycle: CTL and AERO. The two differ by anthropogenic emissions over Indian Peninsula that is included in AERO. We examine the differences in the onset and withdrawal between CTL and AERO. The results show that, relative to the ISM evolution in CTL, the transition of ISM from spring to fall in AERO exhibits a similar ensemble-mean onset date with larger spread and more abrupt change, and an earlier but more gradual withdrawal. The difference is related to aerosols-induced circulation changes in the pre-monsoon environment, including upward motion from the Ganges basin to Indian Peninsula, and strengthened anticyclonic circulation over the Arabia Sea and eastern Bay of Bengal. The changes in AERO-CTL for the developed monsoon period feature a northward shift of monsoon flow such that westerly within 10°-20°N is weaker but the tropical ITCZ (0°-10°N) and the local meridional circulation over northern India are stronger. The earlier monsoon withdrawal in AERO relative to CTL is attributed to the aerosol induced anticyclonic flow within 10°-25°N and cyclonic flow within 0°-10°N over eastern India and Bay of Bengal that resemble the transitional changes in the monsoon withdrawal. The anthropogenic aerosols also cause a 16% (32%) increase in concentration (AOD) by natural dust over India that is transported from the Middle East by aerosols-induced westerly wind in the pre-monsoon season.
Evaluation of TGF-β isoforms based on selected clinical parameters in asthmatic patients.
Authors: Koćwin Marcelina , Jonakowski Mateusz , Majos Alicja , Szemraj Janusz , Kuna Piotr , Panek Michał 
Published: February 2023

Abstract
Introduction: The Transforming Growth Factor β (TGF-β) has attracted particular attention from researchers in the context of the pathogenesis and development of asthma and allergic diseases. Undoubtedly, TGF-β is one of the main cytokines involved in mediating inflammation and bronchial remodeling. It stimulates fibroblasts and myofibroblasts, and regulates processes of extracellular matrix remodeling, thus contributing to fibrosis and bronchial remodeling. In long-term inflammation, the airways become stiffened and airflow is impaired, which is sometimes reflected by lower values of spirometric parameters. What may also be observed in aging organs are intensified fibrotic processes.
Methods: The aim of the study was to evaluate the correlation between concentrations of all the TGF-β1-3 isoforms and selected clinical parameters, including pulmonary function indices assessed by spirometry.The study included 41 asthmatic patients and 28 healthy volunteers recruited from the Department of Allergology and the Allergy and Pulmonology Outpatient Clinic of the N. Barlicki University Teaching Hospital No. 1 in Lodz. The participants underwent a full medical examination and spirometry, and blood samples were collected from them for serum TGF-β levels. Individual isoforms of TGF-β1, TGF-β2 and TGF-β3 were determined by ELISA. The data obtained were then subjected to statistical analysis using Student's t-test, the Mann-Whitney U-test, Fisher's t-test, Pearson's correlation.
Results: The obtained results show significantly increased TGF-β1 and TGF-β2 levels among the elderly, both diseased and healthy individuals. Additionally, higher TGF-β1 and TGF-β2 concentrations correlate significantly with a decreased FEV1%/FVC ratio, while TGF-β2 alone also correlates negatively with FEV1 and FVC values.
Conclusion: The TGF-β1 and TGF-β2 isoforms have been shown to be associated with the pathogenesis of asthma. Expression of TGF-β1 and TGF-β2 increases with age. Higher concentrations of TGF-β1 and TGF-β2 significantly translate into worsening spirometric values. It is worth continuing research on TGF-β as a potential marker of remodeling in asthma.
ChIP- based nuclear DNA isolation for genome sequencing in Pyropia to remove bacterial and cytosol DNA contamination
Authors: zhang zehao , Wang Junhao , Zhang Xiaoqian , Guan Xiaowei , Mao Yunxiang , Poetsch Ansgar , Wang Dongmei 
Published: February 2023

Abstract
Contamination from epiphytic bacteria and cytosolic DNA (plastid and mitochondrion) is challenging the accuracy of genome-wide analysis of nori-producing marine seaweed Pyropia yezoensis. Unlike bacteria and organellar DNA, Pyropia nuclear DNA is tightly associated with histone proteins. In this study, we applied Chromatin Immuno-precipitation (ChIP) of histone H3 to isolate nuclear DNA followed by high-throughput sequencing. More than 99.5% of ChIP-sequencing data are successfully aligned to the reference nuclear genome, remarkably higher than the ones from direct-extraction and nuclei-extraction data in which 40%-50% are from plastid. The proportion of data that mapped to the bacterial database when using ChIP extraction was very low. Additionally, ChIP-data can cover up to 89% of the nuclear genome, higher than direct-extraction data at equal data size and comparable to the latter at equal sequencing depth. The uncovered regions from the three methods are mostly overlapping, suggesting that incomplete sequencing accounts for the missing data, rather than failed chromatin-antibody binding in ChIP-extraction method. This ChIP-extraction method can successfully separate nuclear DNA from cytosolic DNA and bacterial DNA, thus overwhelmingly reducing the sequencing cost in genome resequencing project and provides a strictly purified reference data for genome assembly. The applicability to other macroalgae would makes it a valuable contribution to the algal research community.
Subtelomeric 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) copy number variation confers glyphosate resistance in Eleusine indica
Authors: Zhang Chun , Johnson Nicholas , Hall Nathan , Tian Xingshan , Yu Qin , Patterson Eric 
Published: February 2023

Abstract
Genomic structural variation (SV) can have profound effects on an organism’s evolution, often serving as a novel source of genetic variation. Gene copy number variation (CNV), a specific form of SV, has repeatedly been associated with adaptive evolution in eukaryotes, especially to biotic and abiotic stresses. Resistance to the most widely used herbicide, glyphosate, has evolved through target-site CNV in many weedy plant species, including the economically important cosmopolitan grass, Eleusine indica (goosegrass); however, the origin and mechanisms of these resistance CNVs remain elusive in many weed species due to limited genetic and genomics resources. In order to study the target site CNV in goosegrass, we generated high-quality reference genomes for both glyphosate-susceptible and -resistant individuals, fine assembled the duplication of glyphosate's target site gene enolpyruvylshikimate-3-phosphate synthase (EPSPS), and revealed a novel rearrangement of EPSPS into the subtelomeric region of the chromosomes, ultimately leading to herbicide resistance evolution. This discovery adds to the limited knowledge of the importance of subtelomeres as rearrangement hotspots and novel variation generators as well as provides an example of yet another unique pathway for the formation of CNVs in plants.
Usefulness of mirtazapine and SSRIs in late-life depression. Post hoc analysis of the GUNDAM study.
Authors: Kato Masaki , Baba Hajime , Takekita Yoshiteru , Naito Minami , Koshikawa Yosuke , Bandou Hiroki , Kinoshita Toshihiko 
Published: February 2023

Abstract
Objective
Mirtazapine and SSRIs are widely prescribed as first-line agents for late-life depression. However, evidence for these drugs is mostly based on non-elderly patients. Therefore, we reanalyzed a randomized controlled trial of mirtazapine versus SSRIs for depression in a sub-population of late-life patients.
Methods
A randomized controlled trial was conducted with 141 patients, of whom 41 were elderly, and 100 were non-elderly. This study compared SSRIs and mirtazapine in late-life depression, examined late-onset and early adult-onset separately, and compared elderly and non-elderly patients for each drug. Treatment effects and adverse events were assessed using the Hamilton Depression Rating Scale and the Udvalg for Kliniske Undersøgelserside effect rating scale, respectively.
Results
In late-life depression, mirtazapine showed faster HAM-D total score improvement (3.3 points difference, p=0.021) and higher improvement in insomnia (1.7 points difference, p=0.001) and appetite (1.2 points difference, p=0.020). Similar findings were observed for late-onset depression with the HAM-D total score (4.3 points difference, p=0.007) and appetite (0.9 points difference, p=0.004), favoring mirtazapine. Depressive symptoms were generally less improved in late-life depression than in non-late-life depression. Regarding the effect of mirtazapine on appetite, late-life depression showed greater improvement (0.7 points difference, p=0.008). Nausea and micturition disturbances were more common with SSRIs in late-life depression than in non-late-lifedepression. In contrast, somnolence was less common in late-life depression with mirtazapine.
Conclusion
The potential usefulness of mirtazapine in elderly patients was demonstrated. The results also showed differences in the treatment response to SSRIs and mirtazapine between elderly and non-elderly patients.
Earthquake-induced soil landslides: volume estimates and uncertainties with the existing scaling exponents
Authors: Yunus Ali P. , Xinyu Chen , Catani Filippo , Subramaniam Srikrishnan Siva , Fan Xuanmei , Jie Dou , Sajinkumar K. S. , Gupta Ankita , Avtar Ram 
Published: February 2023

Abstract
Quantifying landslide volumes in earthquake affected areas is critical to understand the orogenic processes and their surface effects at different spatio-temporal scales. Here, we build an accurate scaling relationship to estimate the volume of soil landslides based on 1 m pre- and post-event LiDAR elevation models. On compiling an inventory of 1719 landslides in Mw 6.6 Hokkaido earthquake epicentral region, we find that the volume of soil landslides can be estimated by γ = 1.15–1.18. The total volume of eroded debris from Hokkaido catchments based on this new scaling relationship is estimated as 64–72 million m3. Uncertainties from the existing scaling relationships are found large except for the one found in recent literature 1. Based on the GNSS data approximation, we noticed that the co-seismic uplift volume is smaller than the eroded volume, suggesting that frequent large earthquakes may be counterbalancing the topographic uplift through erosion by landslides.