bluuebunny/crossref_metadata_2025_split huggingface dataset:
The use of steroids in treating chylothorax following cardiac surgery in children: a unique perspective
Authors: Saad Dima , Makarem Adham , Fakhri Ghina , Al Amin Farah , Bitar Fadi , El Rassi Issam , Arabi Mariam 
Published: April 2022

AbstractBackground:Chylothorax is the accumulation of chyle fluid in the pleural space. The incidence of chylothorax is quite common post-cardiac surgeries in pediatrics especially in Fontan procedures. Although several treatment lines are known for the management of chylothorax, steroids were scarcely reported as a treatment option. We present a unique case of a 4-year-old child who underwent Fontan procedure and suffered a long-term consequence of chylothorax. The chylothorax only fully resolved after introducing corticosteroids as part of her management.Methods:A literature review about management of chylothorax post-cardiac surgery in children using Ovid Medline (19462021), PubMed, and google scholar was performed.Conclusion:Conservative management without additional surgical intervention is adequate in most patients. Additionally, somatostatin can be used with variable success rate. However, a few cases mentioned using steroids in such cases. More research and reporting on the use of steroids in the treatment of chylothorax post-cardiac surgeries in children is needed to prove its effectivity. In this article, we describe a case of chylothorax post-Fontan procedure that supports the use of steroids.
Roles of Tidal Cycling, Hyporheic Exchange and Bioirrigation on Metal Release From Estuary Sediments
Authors: Liu Y. , Reible D. , Hussain F. 
Published: April 2022

AbstractA numerical model is developed to investigate metal release from estuarine sediments. The model includes three‐dimensional (3D) large‐eddy simulation of water above the sediment‐water interface, 3D advective and diffusive transport within sediments by both physical and biological processes (bioturbation and bioirrigation), and biogeochemical processes within the sediment including reduction of electron acceptors, acid‐base reactions, and metal sorption and precipitation. The model was applied to explore the influence of overlying water chemistry and sediment chemical, physical and biological processes on metal release from sediments. Overlying water conditions (pH, salinity, oxygen saturation) may vary diurnally due to tidal cycling and control the short‐term release of metals, while over longer times (months), metals are controlled by long‐term averages of sediment convective processes (groundwater upwelling, hyporheic exchange and bioirrigation). Metal release is significantly enhanced when there is bioroughness and bioirrigation due to local oxidation of surficial sediments.
Single-cell RNA sequencing analysis of human bone-marrow-derived mesenchymal stem cells and functional subpopulation identification
Authors: Xie Zhongyu , Yu Wenhui , Ye Guiwen , Li Jinteng , Zheng Guan , Liu Wenjie , Lin Jiajie , Su Zepeng , Che Yunshu , Ye Feng , Zhang Zhaoqiang , Wang Peng , Wu Yanfeng , Shen Huiyong 
Published: April 2022

AbstractMesenchymal stem cells (MSCs) are a common kind of multipotent cell in vivo, but their heterogeneity limits their further applications. To identify MSC subpopulations and clarify their relationships, we performed cell mapping of bone-marrow-derived MSCs through single-cell RNA (scRNA) sequencing. In our study, three main subpopulations, namely, the stemness subpopulation, functional subpopulation, and proliferative subpopulation, were identified using marker genes and further bioinformatic analyses. Developmental trajectory analysis showed that the stemness subpopulation was the root and then became either the functional subpopulation or the proliferative subpopulation. The functional subpopulation showed stronger immunoregulatory and osteogenic differentiation abilities but lower proliferation and adipogenic differentiation. MSCs at different passages or isolated from different donors exhibited distinct cell mapping profiles, which accounted for their corresponding different functions. This study provides new insight into the biological features and clinical use of MSCs at the single-cell level, which may contribute to expanding their application in the clinic.
The impact of perinatal inflammation on the electroencephalogram in preterm infants: a systematic review
Authors: Giraud Antoine , Stephens Carol M. , Boylan Geraldine B. , Walsh Brian H. 
Published: April 2022

AbstractBackgroundTo summarise the association between perinatal inflammation (PI) exposure and electroencephalography (EEG) features in preterm infants.MethodsThis systematic review included clinical studies of preterm infants born <37 weeks of gestational age (GA), who had both a PI exposure and an EEG assessment performed during the neonatal period. Studies were identified from Medline and Embase databases on the 15th of September 2021. PI was defined by histological chorioamnionitis, clinical chorioamnionitis, or early-onset neonatal infection (EONI). The risk of bias in included studies was assessed using the Joanna Briggs Institute (JBI) appraisal tool. A narrative approach was used to synthesise results. This review followed the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) 2020 statement.ResultsTwo cross-sectional studies enrolling 130 preterm children born <32 weeks of GA assessed with one-channel amplitude-integrated EEG (aEEG) during the first four days of life were included. A PI exposure was described in 39 (30%) infants and was associated with a decrease in amplitude and a reduced incidence of sleep-wake cycling patterns.ConclusionThese results should be interpreted with caution because of the small number of included studies and their heterogeneity. Further clinical studies evaluating the association of PI with EEG findings are needed.ImpactA method to assess developmental trajectories following perinatal inflammation is required.Insufficient data exist to determine EEG features associated with perinatal inflammation.Further clinical studies evaluating this association are needed.
Reduced bacterial mortality and enhanced viral productivity during sinking in the ocean
Authors: Wei Wei , Chen Xiaowei , Weinbauer Markus G , Jiao Nianzhi , Zhang Rui 
Published: April 2022

Abstract
Particle sinking is an important process in the ocean, influencing the biogeochemical cycle and driving the long-term preservation of carbon into the deep sea via the biological pump. However, as an important component of marine ecosystems, the role of viruses during sinking is still poorly understood. Therefore, we performed a series of transplantation experiments in the South China Sea to simulate environmental changes during sinking and investigate their effects on viral eco-dynamics and life strategy. Our study demonstrated increased viral production but decreased virus-mediated bacterial mortality after transplantation. A larger burst size and switch from the lysogenic to lytic strategy were shown to contribute to enhanced viral productivity. We provide experimental evidence that surface viral ecological characteristics changed dramatically after transplantation into deep-sea waters, indicating a potential importance of viruses during vertical sinking in the ocean. This effect probably provides positive feedback on the efficiency of the biological pump.
Knowledge of undergraduate dental students regarding management of caries lesions
Authors: Jablonski-Momeni Anahita , Korbmacher-Steiner Heike , Temming Alexa , Wernke Pia , Heinzel-Gutenbrunner Monika , Haak Rainer , Krause Felix 
Published: April 2022

Abstract
Objectives
Understanding of lifelong control of disease processes associated with caries and its management is an essential part of dental education. This study evaluated the dental students’ knowledge of caries diagnosis and management using the International Caries Classification and Management System (ICCMS).

Methods
A survey was conducted among undergraduate dental students at two dental schools, attending the sixth (centre 1) and seventh semester (centre 2), respectively. Medical histories, clinical images and radiographs of 12 patients were compiled as anonymous cases. For each case, a specific lesion was to be assessed. In addition, the students should determine the patient’s caries risk and select a treatment option. An expert report (consensus decision) was used as the reference standard. For statistical analysis, kappa statistics and binomial tests were used.

Results
A total of 46 students participated in this study. The percentage of agreement of responses to the reference was: centre 1: 40.7–51.3%, centre 2: 57.9–67.9%. The corresponding Kappa values were: centre 1: 0.073–0.175, centre 2: 0.315–0.432. Overall, students tended to underestimate the codes compared to the reference standard (p < 0.001).

Conclusion
Introducing systematic content about caries diagnosis and management such as ICDAS and ICCMS in the learning objectives of undergraduate dental students can be proposed. However, in order to improve diagnosis and enable a more reliable choice of treatment options, attention should also be given to the way they are didactically taught.
IL-1β-activated mTORC2 promotes accumulation of IFN-γ+ γδ T cells by upregulating CXCR3 to restrict hepatic fibrosis
Authors: Liu Qihui , Yang Quanli , Wu Zengfeng , Chen Yanfang , Xu Miaomiao , Zhang Hua , Zhao Jiliang , Liu Zonghua , Guan Zerong , Luo Jing , Li Zhi-yong , Sun Guodong , Wen Qiong , Xu Yan , Li Zhenhua , Chen Kebing , Ben Xiaosong , He Wanchun , Li Xueshi , Yin Zhinan , Hao Jianlei , Lu Ligong 
Published: April 2022

AbstractLiver fibrosis represents a severe stage of liver damage, with hallmarks of inflammation, hepatic stellate cell activation, and extracellular matrix accumulation. Although previous studies demonstrated γδ T cells are involved in liver fibrosis, the precise role and mechanisms of γδ T cells migrating to fibrotic liver have not been elucidated. Here, we aim to investigate the functional subsets of γδ T cells in hepatic fibrosis and to further explore the underlying causes and drivers of migration. In this study, we observed that γδ T cells accumulate in fibrotic liver. Adoptive transfer of γδ T, especially Vγ4 γδ T subset, can significantly alleviate liver fibrosis. In addition, CCl4 treatment also leads to activation of mTOR signaling in γδ T cells. Genetic deletion of the Rictor gene, but not Raptor, in γδ T cells markedly exacerbated liver fibrosis. Mechanistically, CCl4-induced liver injury causes macrophage accumulation in the liver, and IL-1β produced by macrophages promotes mTORC2 signaling activation in γδ T cells, which upregulates T-bet expression and eventually promotes CXCR3 transcription to drive γδ T cell migration. Moreover, hepatic γδ T cells ameliorated liver fibrosis by cytotoxicity against activated hepatic stellate cells in FasL-dependent manner, and secrete IFN-γ to inhibit the differentiation of pro-fibrotic Th17 cells. Thus, IL-1β-activated mTORC2 signaling in γδ T cells upregulates CXCR3 expression, which is critical for IFN-γ+ γδ T cells migration into the liver and amelioration of liver fibrosis. Our findings indicate that targeting the mTORC2 or CXCR3 in γδ T cells could be considered as a promising approach for γδ T cell immunotherapy against liver fibrosis.
Class I HDAC overexpression promotes temozolomide resistance in glioma cells by regulating RAD18 expression
Authors: Hanisch Daniela , Krumm Andrea , Diehl Tamara , Stork Carla M. , Dejung Mario , Butter Falk , Kim Ella , Brenner Walburgis , Fritz Gerhard , Hofmann Thomas G. , Roos Wynand P. 
Published: April 2022

AbstractOverexpression of histone deacetylases (HDACs) in cancer commonly causes resistance to genotoxic-based therapies. Here, we report on the novel mechanism whereby overexpressed class I HDACs increase the resistance of glioblastoma cells to the SN1 methylating agent temozolomide (TMZ). The chemotherapeutic TMZ triggers the activation of the DNA damage response (DDR) in resistant glioma cells, leading to DNA lesion bypass and cellular survival. Mass spectrometry analysis revealed that the catalytic activity of class I HDACs stimulates the expression of the E3 ubiquitin ligase RAD18. Furthermore, the data showed that RAD18 is part of the O6-methylguanine-induced DDR as TMZ induces the formation of RAD18 foci at sites of DNA damage. Downregulation of RAD18 by HDAC inhibition prevented glioma cells from activating the DDR upon TMZ exposure. Lastly, RAD18 or O6-methylguanine-DNA methyltransferase (MGMT) overexpression abolished the sensitization effect of HDAC inhibition on TMZ-exposed glioma cells. Our study describes a mechanism whereby class I HDAC overexpression in glioma cells causes resistance to TMZ treatment. HDACs accomplish this by promoting the bypass of O6-methylguanine DNA lesions via enhancing RAD18 expression. It also provides a treatment option with HDAC inhibition to undermine this mechanism.
Inhibition of RIPK1 by ZJU-37 promotes oligodendrocyte progenitor proliferation and remyelination via NF-κB pathway
Authors: Ma Xiao-Ru , Yang Shu-Ying , Zheng Shuang-Shuang , Yan Huan-Huan , Gu Hui-Min , Wang Fan , Wu Yang , Dong Zhao-Jun , Wang Di-Xian , Wang Yue , Meng Xianhui , Sun Jie , Xia Hong-Guang , Zhao Jing-Wei 
Published: April 2022

AbstractReceptor interacting serine/threonine protein kinase 1 (RIPK1) activation and necroptosis have been genetically and mechanistically linked with human multiple sclerosis and neurodegenerative diseases for which demyelination is a common key pathology. Demyelination can be healed through remyelination which is mediated by new oligodendrocytes derived from the adult oligodendrocyte progenitor cells (OPCs). Unfortunately, the efficiency of remyelination declines with progressive aging partially due to the depletion of OPCs following chronic or repeated demyelination. However, to our knowledge, so far there is no drug which enhances proliferation of OPCs, and it is unknown whether inhibiting RIPK1 activity directly affect OPCs, the central player of remyelination. Using TNFα induced RIPK1-dependent necroptosis in Jurkat FADD−/− cells as a cell death assay, we screened from 2112 FDA-approved drugs and the drug candidates of new RIPK1 inhibitors selected by ourselves, and identified ZJU-37, a small molecule modified by introducing an amide bond to Nec-1s, is a new RIPK1 kinase inhibitor with higher potency than Nec-1s which has the best reported potency. We unveil in addition to protecting myelin from demyelination and axons from degeneration, ZJU-37 exhibits a new role on promoting proliferation of OPCs and enhancing remyelination by inhibiting RIPK1 kinase activity with higher potency than Nec-1s. Mechanistically, ZJU-37 promotes proliferation of OPCs by enhancing the transcription of platelet derived growth factor receptor alpha via NF-κB pathway. This work identifies ZJU-37 as a new drug candidate which enhances remyelination by promoting proliferation of OPCs, paving the way for a potential drug to enhance myelin repair.
Smart hydrogels with wide visible color tunability
Authors: Wen Guo-Yu , Zhou Xing-Long , Tian Xiao-Yu , Xie Rui , Ju Xiao-Jie , Liu Zhuang , Faraj Yousef , Wang Wei , Chu Liang-Yin 
Published: April 2022

AbstractPigmentary coloration can produce viewing angle-independent uniform colors via light absorption by chromophores. However, due to the limited diversity in the changes of the molecular configuration of chromophores to undergo color change, the existing materials cannot produce a wide range of visible colors with tunable color saturation and transmittance. Herein, we propose a novel strategy to create materials with a wide visible color range and highly tunable color saturation and transmittance. We fabricated a hydrogel with poly (acrylamide-co-dopamine acrylamide) networks swollen with Fe3+-containing glycerol/water in which the covalently crosslinked polyacrylamide backbone with pendant catechols can ensure that the hydrogel maintains a very stable shape. Hydrogels containing adjustable catechol-Fe3+ coordination bonds with flexible light-interacting configuration changes can display a wide range of visible colors based on the complementary color principle. The catechol-Fe3+ complexes can dynamically switch between noncoordinated and mono-, bis- and tris-coordinated states to harvest light energy from a specific wavelength across the whole visible spectrum. Therefore, these hydrogels can be yellow, green, blue, and red, covering the three primary colors. Moreover, color saturation and transmittance can be flexibly manipulated by simply adjusting the Fe3+ content in the hydrogel networks. The versatility of these smart hydrogels has been demonstrated through diverse applications, including optical filters for color regulation and colorimetric sensors for detecting UV light and chemical vapors. This proposed smart hydrogel provides a universal color-switchable platform for the development of multifunctional optical systems such as optical filters, sensors, and detectors.
Harnessing phosphonate antibiotics argolaphos biosynthesis enables a synthetic biology-based green synthesis of glyphosate
Authors: Chu Leixia , Luo Xiaoxia , Zhu Taoting , Cao Yingying , Zhang Lili , Deng Zixin , Gao Jiangtao 
Published: April 2022

AbstractGlyphosate is a widely used herbicide with an annual production of more than one million tons globally. Current commercialized production processes of glyphosate are generally associated with manufacturing hazards and toxic wastes. Recently, many countries have strengthened environmental supervision and law enforcement on glyphosate manufacturing. Therefore, a green source of glyphosate is required. Here, we characterize the genes required for producing aminomethylphosphonate (AMP), one of the intermediates in the biosynthesis of the potent antibiotics argolaphos. We apply a synthetic biology strategy to improve AMP production in Streptomyces lividans, with fermentation titers of 52 mg L-1, a 500-fold improvement over the original strain. Furthermore, we develop an efficient and practical chemical process for converting AMP to glyphosate. Our findings highlight one greenness-driven alternative in the production of glyphosate.
Current progress and open challenges for applying deep learning across the biosciences
Authors: Sapoval Nicolae , Aghazadeh Amirali , Nute Michael G. , Antunes Dinler A. , Balaji Advait , Baraniuk Richard , Barberan C. J. , Dannenfelser Ruth , Dun Chen , Edrisi Mohammadamin , Elworth R. A. Leo , Kille Bryce , Kyrillidis Anastasios , Nakhleh Luay , Wolfe Cameron R. , Yan Zhi , Yao Vicky , Treangen Todd J. 
Published: April 2022

AbstractDeep Learning (DL) has recently enabled unprecedented advances in one of the grand challenges in computational biology: the half-century-old problem of protein structure prediction. In this paper we discuss recent advances, limitations, and future perspectives of DL on five broad areas: protein structure prediction, protein function prediction, genome engineering, systems biology and data integration, and phylogenetic inference. We discuss each application area and cover the main bottlenecks of DL approaches, such as training data, problem scope, and the ability to leverage existing DL architectures in new contexts. To conclude, we provide a summary of the subject-specific and general challenges for DL across the biosciences.
AF2Complex predicts direct physical interactions in multimeric proteins with deep learning
Authors: Gao Mu , Nakajima An Davi , Parks Jerry M. , Skolnick Jeffrey 
Published: April 2022

AbstractAccurate descriptions of protein-protein interactions are essential for understanding biological systems. Remarkably accurate atomic structures have been recently computed for individual proteins by AlphaFold2 (AF2). Here, we demonstrate that the same neural network models from AF2 developed for single protein sequences can be adapted to predict the structures of multimeric protein complexes without retraining. In contrast to common approaches, our method, AF2Complex, does not require paired multiple sequence alignments. It achieves higher accuracy than some complex protein-protein docking strategies and provides a significant improvement over AF-Multimer, a development of AlphaFold for multimeric proteins. Moreover, we introduce metrics for predicting direct protein-protein interactions between arbitrary protein pairs and validate AF2Complex on some challenging benchmark sets and the E. coli proteome. Lastly, using the cytochrome c biogenesis system I as an example, we present high-confidence models of three sought-after assemblies formed by eight members of this system.
BRCA2-DSS1 interaction is dispensable for RAD51 recruitment at replication-induced and meiotic DNA double strand breaks
Authors: Mishra Arun Prakash , Hartford Suzanne A. , Sahu Sounak , Klarmann Kimberly , Chittela Rajani Kant , Biswas Kajal , Jeon Albert B. , Martin Betty K. , Burkett Sandra , Southon Eileen , Reid Susan , Albaugh Mary E. , Karim Baktiar , Tessarollo Lino , Keller Jonathan R. , Sharan Shyam K. 
Published: April 2022

AbstractThe interaction between tumor suppressor BRCA2 and DSS1 is essential for RAD51 recruitment and repair of DNA double stand breaks (DSBs) by homologous recombination (HR). We have generated mice with a leucine to proline substitution at position 2431 of BRCA2, which disrupts this interaction. Although a significant number of mutant mice die during embryogenesis, some homozygous and hemizygous mutant mice undergo normal postnatal development. Despite lack of radiation induced RAD51 foci formation and a severe HR defect in somatic cells, mutant mice are fertile and exhibit normal RAD51 recruitment during meiosis. We hypothesize that the presence of homologous chromosomes in close proximity during early prophase I may compensate for the defect in BRCA2-DSS1 interaction. We show the restoration of RAD51 foci in mutant cells when Topoisomerase I inhibitor-induced single strand breaks are converted into DSBs during DNA replication. We also partially rescue the HR defect by tethering the donor DNA to the site of DSBs using streptavidin-fused Cas9. Our findings demonstrate that the BRCA2-DSS1 complex is dispensable for RAD51 loading when the homologous DNA is close to the DSB.
Exploration of the dynamic interplay between lipids and membrane proteins by hydrostatic pressure
Authors: Pozza Alexandre , Giraud François , Cece Quentin , Casiraghi Marina , Point Elodie , Damian Marjorie , Le Bon Christel , Moncoq Karine , Banères Jean-Louis , Lescop Ewen , Catoire Laurent J. 
Published: April 2022

AbstractCell membranes represent a complex and variable medium in time and space of lipids and proteins. Their physico-chemical properties are determined by lipid components which can in turn influence the biological function of membranes. Here, we used hydrostatic pressure to study the close dynamic relationships between lipids and membrane proteins. Experiments on the β–barrel OmpX and the α–helical BLT2 G Protein-Coupled Receptor in nanodiscs of different lipid compositions reveal conformational landscapes intimately linked to pressure and lipids. Pressure can modify the conformational landscape of the membrane protein per se, but also increases the gelation of lipids, both being monitored simultaneously at high atomic resolution by NMR. Our study also clearly shows that a membrane protein can modulate, at least locally, the fluidity of the bilayer. The strategy proposed herein opens new perspectives to scrutinize the dynamic interplay between membrane proteins and their surrounding lipids.