bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthetic Rain Models and Optical Flow Algorithms for Improving the Resolution of Rain Attenuation Time Series Simulated From Numerical Weather Prediction
Authors: Razavian Mojtaba , Oestges Claude , Vanhoenacker‐Janvier Danielle 
Published: December 2022

AbstractNew generation of satellite system communication is moving toward frequencies above 20 GHz and non‐geostationary satellites. In order to guaranty the quality of service, specific Fade Mitigation Techniques have to be applied, like Advanced Coding and Modulation (ACM). In order to accurately design ACM, time series of attenuation should be used. As there are no measurements available, the simulation of attenuation times series for non‐geostationary earth‐space links becomes critical. This paper presents a model consisting in a combination of a Numerical Weather Prediction model (Weather Research and Forecasting), a synthetic rain cell model MultiEXCELL and Optical Flow techniques. It gives an efficient method to generate more realistic rain attenuation time series. Long‐term CCDF statistics of simulated attenuation data are validated by comparison with the Alphasat measurement data over 2 years at Louvain‐la‐Neuve ground station.
The times they are a-changin’: a proposal on how brain flexibility goes beyond the obvious to include the concepts of “upward” and “downward” to neuroplasticity
Authors: Diniz Cassiano Ricardo Alves Faria , Crestani Ana Paula 
Published: December 2022

AbstractSince the brain was found to be somehow flexible, plastic, researchers worldwide have been trying to comprehend its fundamentals to better understand the brain itself, make predictions, disentangle the neurobiology of brain diseases, and finally propose up-to-date treatments. Neuroplasticity is simple as a concept, but extremely complex when it comes to its mechanisms. This review aims to bring to light an aspect about neuroplasticity that is often not given enough attention as it should, the fact that the brain’s ability to change would include its ability to disconnect synapses. So, neuronal shrinkage, decrease in spine density or dendritic complexity should be included within the concept of neuroplasticity as part of its mechanisms, not as an impairment of it. To that end, we extensively describe a variety of studies involving topics such as neurodevelopment, aging, stress, memory and homeostatic plasticity to highlight how the weakening and disconnection of synapses organically permeate the brain in so many ways as a good practice of its intrinsic physiology. Therefore, we propose to break down neuroplasticity into two sub-concepts, “upward neuroplasticity” for changes related to synaptic construction and “downward neuroplasticity” for changes related to synaptic deconstruction. With these sub-concepts, neuroplasticity could be better understood from a bigger landscape as a vector in which both directions could be taken for the brain to flexibly adapt to certain demands. Such a paradigm shift would allow a better understanding of the concept of neuroplasticity to avoid any data interpretation bias, once it makes clear that there is no morality with regard to the organic and physiological changes that involve dynamic biological systems as seen in the brain.
HPV status represents dominant trait driving delineation of survival-associated gene co-expression networks in head and neck cancer
Authors: Mehdi Ahmed M. , Zhou Chenhao , Turrell Gavin , Walpole Euan , Porceddu Sandro , Frazer Ian H. , Chandra Janin 
Published: December 2022

AbstractIntegration of high-dimensional tumor gene expression data with clinicopathological data can increase our understanding of disease diversity, enable retrospective patient stratification, and identify new potential biomarkers and therapeutic targets. Using a systems biology approach, we provide a holistic overview of gene co-expression networks in head and neck squamous cell carcinomas (HNSCC). Weighted gene co-expression network analysis of HNSCC RNA sequencing data from 519 patients from The Cancer Genome Atlas (TCGA) was used to determine correlates of 5-year survival, using regression tree-based optimal threshold calculations. Survival-associated gene sets were transformed to gene set scores that were assessed for correlation with clinicopathological data. We identified 8 gene co-expression modules for HNSCC tumors, each of which contained co-expressed genes associated significantly with 5-year survival. Survival-associated co-expression gene signatures correlated dominantly with tumor HPV and p16 status. Network analysis identified that survival was associated with signaling networks of infection, immunity, epithelial-mesenchymal transition (EMT), hypoxia, glycolysis, focal adhesion, extracellular matrix, MYC signaling, autophagy and transcriptional regulation. EMT-associated gene signatures were expressed dominantly in fibroblasts, and cancer-associated fibroblasts were inversely correlated with immune activity. Interestingly, a high Immune Suppression Score based on expression of 21 genes associated with immune inhibition and including immune checkpoints, cytokines and regulatory T cell factors, was also associated with increased survival probability, and was significantly higher in HPV+ HNSCC. Networks associated with HNSCC survival were further associated with survival in cervical cancer, melanoma and lung cancer. This study defines 5129 genes associated with HNSCC survival, organized into co-expressed networks, their correlation with clinicopathological data, and with gene expression data from other malignant diseases, and provides a source for the discovery of biomarkers and novel therapies for HNSCC.
High-precision mapping reveals rare N6-deoxyadenosine methylation in the mammalian genome
Authors: Chen Li-Qian , Zhang Zhang , Chen Hong-Xuan , Xi Jian-Fei , Liu Xue-Hong , Ma Dong-Zhao , Zhong Yu-Hao , Ng Wen Hui , Chen Tao , Mak Daniel W. , Chen Qi , Chen Yao-Qing , Luo Guan-Zheng 
Published: December 2022

AbstractN6-deoxyadenosine methylation (6mA) is the most widespread type of DNA modification in prokaryotes and is also abundantly distributed in some unicellular eukaryotes. However, 6mA levels are remarkably low in mammals. The lack of a precise and comprehensive mapping method has hindered more advanced investigations of 6mA. Here, we report a new method MM-seq (modification-induced mismatch sequencing) for genome-wide 6mA mapping based on a novel detection principle. We found that modified DNA bases are prone to form a local open region that allows capture by antibody, for example, via a DNA breathing or base-flipping mechanism. Specified endonuclease or exonuclease can recognize the antibody-stabilized mismatch-like structure and mark the exact modified sites for sequencing readout. Using this method, we examined the genomic positions of 6mA in bacteria (E. coli), green algae (C. reinhardtii), and mammalian cells (HEK239T, Huh7, and HeLa cells). In contrast to bacteria and green algae, human cells possess a very limited number of 6mA sites which are sporadically distributed across the genome of different cell types. After knocking out the RNA m6A methyltransferase METTL3 in mouse ES cells, 6mA becomes mostly diminished. Our results imply that rare 6mA in the mammalian genome is introduced by RNA m6A machinery via a non-targeted mechanism.
The neglected role of micronutrients in predicting soil microbial structure
Authors: Peng Ziheng , Liang Chunling , Gao Min , Qiu Yu , Pan Yanjing , Gao Hang , Liu Yu , Li Xiaomeng , Wei Gehong , Jiao Shuo 
Published: December 2022

AbstractPredicting the distribution patterns of soil microbial communities requires consideration of more environmental drivers. The effects of soil micronutrients on composition of microbial communities are largely unknown despite micronutrients closely relating to soil fertility and plant communities. Here we used data from 228 agricultural fields to identify the importance of micronutrients (iron, zinc, copper and manganese) in shaping structure of soil microbial communities (bacteria, fungi and protist) along latitudinal gradient over 3400 km, across diverse edaphic conditions and climatic gradients. We found that micronutrients explained more variations in the structure of microbial communities than macronutrients in maize soils. Moreover, micronutrients, particularly iron and copper, explained a unique percentage of the variation in structure of microbial communities in maize soils even after controlling for climate, soil physicochemical properties and macronutrients, but these effects were stronger for fungi and protist than for bacteria. The ability of micronutrients to predict the structure of soil microbial communities declined greatly in paddy soils. Machine learning approach showed that the addition of micronutrients substantially increased the predictive power by 9–17% in predicting the structure of soil microbial communities with up to 69–78% accuracy. These results highlighted the considerable contributions of soil micronutrients to microbial community structure, and advocated that soil micronutrients should be considered when predicting the structure of microbial communities in a changing world.
Dislocation-position fluctuations in solid 4He as collective variables in a quantum crystal
Authors: de Koning Maurice , Cai Wei 
Published: December 2022

AbstractQuantum behavior at mesoscopic length scales is of significant interest, both from a fundamental-physics standpoint, as well as in the context of technological advances. In this light, the description of collective variables comprising large numbers of atoms, but nevertheless displaying non-classical behavior, is a fundamental problem. Here, we show that an effective-Hamiltonian approach for such variables, as has been applied to describe the quantum behavior of coupled qubit/oscillator systems, can also be very useful in understanding intrinsic behavior of quantum materials. We consider lattice dislocations – naturally occurring mesoscopic line defects in crystals – in the prototypical bosonic quantum crystal, solid4He. For this purpose, we map fully atomistic quantum simulations onto effective one-dimensional Hamiltonians in which the collective dislocation-position variables are represented as interacting, massive quantum particles. The results provide quantitative understanding of several experimental observations in solid4He.
Predicting stress response and improved protein overproduction in Bacillus subtilis
Authors: Tibocha-Bonilla Juan D. , Zuñiga Cristal , Lekbua Asama , Lloyd Colton , Rychel Kevin , Short Katie , Zengler Karsten 
Published: December 2022

AbstractBacillus subtilisis a well-characterized microorganism and a model for the study of Gram-positive bacteria. The bacterium can produce proteins at high densities and yields, which has made it valuable for industrial bioproduction. Like other cell factories, metabolic modeling ofB. subtilishas discovered ways to optimize its metabolism toward various applications. The first genome-scale metabolic model (M-model) ofB. subtiliswas published more than a decade ago and has been applied extensively to understand metabolism, to predict growth phenotypes, and served as a template to reconstruct models for other Gram-positive bacteria. However, M-models are ill-suited to simulate the production and secretion of proteins as well as their proteomic response to stress. Thus, a new generation of metabolic models, known as metabolism and gene expression models (ME-models), has been initiated. Here, we describe the reconstruction and validation of a ME model ofB. subtilis,iJT964-ME. This model achieved higher performance scores on the prediction of gene essentiality as compared to the M-model. We successfully validated the model by integrating physiological and omics data associated with gene expression responses to ethanol and salt stress. The model further identified the mechanism by which tryptophan synthesis is upregulated under ethanol stress. Further, we employediJT964-ME to predict amylase production rates under two different growth conditions. We analyzed these flux distributions and identified key metabolic pathways that permitted the increase in amylase production. Models likeiJT964-ME enable the study of proteomic response to stress and the illustrate the potential for optimizing protein production in bacteria.
A repository for the publication and sharing of heterogeneous materials data
Authors: Gong Haiyan , He Jie , Zhang Xiaotong , Duan Lei , Tian Ziqi , Zhao Wei , Gong Fuzhou , Liu Tong , Wang Zongguo , Zhao Haifeng , Jia Weipeng , Zhang Lei , Jiang Xue , Chen Wencong , Liu Shilong , Xiu Hao , Yang Wenjin , Wan Jiawang 
Published: December 2022

AbstractNational Materials Data Management and Service platform (NMDMS) is a materials data repository for the publication and sharing of heterogeneous materials scientific data and follows the FAIR principles: Findable, Accessible, Interoperable, and Reusable. To ensure data are ‘Interoperable, NMDMS uses a user-friendly semi-structured scientific data model, named dynamic container’, to define, exchange, and store heterogeneous scientific data. Then, a personalized yet standardized data submission subsystem, a rigorous project data review and publication subsystem, and a multi-granularity data query and retrieval subsystem collaboratively make data ‘Reusable’, ‘Findable’, and ‘Accessible’. Finally, China’s “National Key R&D Program: Material Genetic Engineering Key Special Project” has adopted NMDMS to publish and share its project data. There are 12,251,040 pieces of data published in NMDMS since 2018, under 87 categories and 1,912 user-defined schemas from 45 projects. The platform has been accessed 908875 times, and 2403,208 pieces of data have been downloaded. In short, NMDMS effectively accelerates the publication and sharing of material project data in China.
Combined analysis of PS-InSAR and hypsometry integral (HI) for comparing seismic vulnerability and assessment of various regions of Pakistan
Authors: Ramzan Uqba , Fan Hong , Aeman Hafsa , Ali Muhammad , A. A. Al-qaness Mohammed 
Published: December 2022

AbstractInSAR-based deformation analysis and the geomorphic hypsometric integral (HI) technique are powerful tools for assessing the susceptibility and comparison of seismic sites to earthquakes. Therefore, this paper mainly focuses on surface deformation analysis associated with the Mw 5.0 earthquake (2019) in Mach and Quetta, Balochistan, Pakistan. Sentinel-1 IW data was used to perform PS-InSAR time series analysis. SRTM DEM of 30 m spatial resolution was utilized for the geomorphic Hypsometry Integral (HI) method. The obtained results of the Interferogram indicate the changes in velocity and vertical displacement during pre-seismic, co-seismic, and post-seismic activity. Integral values were calculated using Hypsometry curves delineating the future probability and comparison of vulnerable seismological sites in Mach, Quetta, Ghazaband, Chamman and surroundings of Balochistan region. The combined results of HI and PS-InSAR revealed that Mach and Quetta regions are in between two lines known as the mature stages. Class 1_moderate (0.35 ≤ HI ≤ 0.52); with an integral value of HIMach = 0.398 and HIQuetta = 0.435 with a modest seismic forthcoming rate in future and susceptible to both erosion/uplifting with a vertical displacement rate more than existing ± 55 mm/year. Class 2_high (HI ˃ 0.53) with the younger and more tectonically active region surrounded by Chaman fault, which possesses a future susceptible tendency towards subsidence more than an existing velocity rate ~ 8 mm/year and Ghazaband fault towards uplifting more than 5–6 mm/year. No region of the study area was found at Monadnock: class 3_Low (HI ˂ 0.35) stabilized condition, all sites are unstable and tectonically active. Therefore, obtained results through combined PS-InSAR and HI techniques can be used for the identification of most vulnerable seismic sites and can ascertain future safe metropolitan planning.
Structure optimization of new tumor-selective Passerini α-acyloxy carboxamides as Caspase-3/7 activators
Authors: Ayoup Mohammed Salah , Wahby Yasmin , Abdel-Hamid Hamida , Abu-Serie Marwa M. , Teleb Mohamed 
Published: December 2022

AbstractSelective elimination of tumors has always been the mainstay of oncology research. The on-going research underlying the cellular apoptotic mechanisms reveal caspases activation, especially the key effector caspase-3, as a personalized tumor-selective therapeutic strategy. Our continued research protocol has exploited new optimized Passerini α-acyloxy carboxamides as efficient apoptotic inducers via caspase-3/7 dependent mechanism with highly selective anticancer profiles. The adopted design rationale relied on excluding structural alerts of previous leads, while merging various pharmacophoric motifs of natural and synthetic caspase activators via optimized one-pot Passerini reaction conditions. The prepared compounds resulting from Passerini reaction were screened for their cytotoxic activities against colorectal Caco-2 and liver HepG-2 cancer cells compared to normal fibroblasts utilizing MTT assay. Notably, all compounds exhibited promising low-range submicromolar IC50 against the studied cancer cell lines, with outstanding tumor selectivity (SI values up to 266). Hence, they were superior to 5-fluorouracil. Notably, 7a, 7g, and 7j conferred the highest potencies against Caco-2 and HepG-2 cells and were selected for further mechanistic studies. Caspas-3/7 activation assay of the hit compounds and flow cytometric analysis of the treated apoptotic cancer cells demonstrated their significant caspase activation potential (up to 4.2 folds) and apoptotic induction capacities (up to 58.7%). Further assessment of Bcl2 expression was performed being a physiological caspase-3 substrate. Herein, the three studied Passerini adducts were able to downregulate Bcl2 in the treated Caco-2 cells. Importantly, the mechanistic studies results of the three hits echoed their preliminary MTT antiproliferative potencies data highlighting their caspase-3 dependent apoptotic induction. Finally, the in silico predicted physicochemical and pharmacokinetic profiles, as well as ligand efficiency metrics were drug-like.
Endotracheal tube biofilm in critically ill patients during the COVID-19 pandemic : description of an underestimated microbiological compartment
Authors: Maldiney Thomas , Pineau Valentin , Neuwirth Catherine , Ouzen Linda , Eberl Isabelle , Jeudy Géraldine , Dalac Sophie , Piroth Lionel , Blot Mathieu , Sautour Marc , Dalle Frédéric , Abdulmalak Caroline , Ter Schiphorst Romain , Pugliesi Paul-Simon , Poussant Thomas , Ogier-Desserrey Agathe , Fournel Isabelle , de Giraud d’Agay Melchior , Jacquier Marine , Labruyère Marie , Aptel François , Roudaut Jean-Baptiste , Vieille Thibault , Andreu Pascal , Prin Sébastien , Charles Pierre-Emmanuel , Hamet Maël , Quenot Jean-Pierre 
Published: December 2022

AbstractBiofilm (BF) growth is believed to play a major role in the development of ventilator-associated pneumonia (VAP) in the intensive care unit. Despite concerted efforts to understand the potential implication of endotracheal tube (ETT)-BF dispersal, clinically relevant data are lacking to better characterize the impact of its mesostructure and microbiological singularity on the occurrence of VAP. We conducted a multicenter, retrospective observational study during the third wave of the COVID-19 pandemic, between March and May 2021. In total, 64 ETTs collected from 61 patients were included in the present BIOPAVIR study. Confocal microscopy acquisitions revealed two main morphological aspects of ETT-deposited BF: (1) a thin, continuous ribbon-shaped aspect, less likely monobacterial and predominantly associated with Enterobacter spp., Streptococcus pneumoniae or Viridans streptococci, and (2) a thicker, discontinuous, mushroom-shaped appearance, more likely characterized by the association of bacterial and fungal species in respiratory samples. The microbiological characterization of ETT-deposited BF found higher acquired resistance in more than 80% of analyzed BF phenotypes, compared to other colonization sites from the patient’s environment. These findings reveal BF as a singular microbiological compartment, and are of added clinical value, with a view to future ETT-deposited BF-based antimicrobial stewardship in critically ill patients.
Trial registration NCT04926493. Retrospectively registered 15 June 2021.
A novel strategy for process optimization of a natural gas liquid recovery unit by replacing Joule–Thomson valve with supersonic separator
Authors: Shoghl Sina Nabati , Naderifar Abbas , Farhadi Fatola , Pazuki Gholamreza 
Published: December 2022

AbstractThe natural gas liquid recovery is an important process in a gas plant to correct hydrocarbon dew point and earn profit. In this study, a natural gas liquid recovery unit operated based on the Joule–Thomson process was investigated and its performance was optimized. To improve the system performance, the plant configuration and intermediate pressure ratio were defined as the variables and maximization of the natural gas liquid recovery rate and maximization of exergy efficiency were defined as the objective functions. To improve the plant performance, the amount of natural gas liquid recovery rate should be increased. To achieve this goal, several scenarios for the intermediate pressure ratio and three new configurations were proposed for the investigated gas plant. In the proposed configurations, the supersonic separators with optimized structures were used instead of the Joule–Thomson process. It was observed that all three proposed configurations improved the natural gas liquid recovery rate compared to the existing configuration. For example, by installing two supersonic separators instead of second and third stage Joule–Thomson valve + low temperature separator, at the optimal operating condition, the natural gas liquid recovery rate increased about 390%. The influence of the intermediate pressure ratio on the phase envelope diagram, exergy efficiency, dew point depression and natural gas liquid recovery rate was also investigated. By comparing the influence of intermediate pressure ratio and modifying the plant configuration on the objective functions, it was observed that the system performance can be further improved by modifying the plant configuration.