bluuebunny/crossref_metadata_2025_split huggingface dataset:
LncRNA NALT1 promotes colorectal cancer progression via targeting PEG10 by sponging microRNA-574-5p
Authors: Ye Mengling , Zhao Lu , Zhang Lu , Wu Siyi , Li Zhao , Qin Yi , Lin Fei , Pan Linghui 
Published: November 2022

AbstractColorectal cancer (CRC) is currently one of the commonest tumors and the main reason for cancer-related deaths worldwide. It has been reported that long non-coding RNAs (lncRNAs) act as important indicators and regulators in various cancers. There is an urgent need to explore new lncRNA biomarkers in CRC, as well as their functions and molecular mechanisms. NALT1 has been implicated in the occurrence of gastric cancer (GC). However, the detailed function and mechanism of NALT1 in CRC progress have not been reported. In this study, RT-qPCR was conducted to detect the expression of NALT1 in 76 CRC patients ranging from stages I through IV. To assess the biological function of NALT1, loss- and gain-of-function experiments were conducted both in vivo and in vitro. Moreover, RNA-seq, bioinformatics analysis, RNA pulldown assay, dual-luciferase reporter, Ago2-RIP, quantitative PCR, Western blot assays, and rescue experiments were performed to reveal the molecular mechanisms of competitive endogenous RNAs (ceRNAs). It was observed that high expression of NALT1 was markedly correlated with advanced cancer stage in the clinic. Functionally, NALT1 downregulation inhibited cell proliferation, migration and invasion, whereas NALT1 overexpression exhibited an opposite trend both in vivo and in vitro. Bioinformatics analysis, RNA pulldown, Ago2-RIP, and luciferase reporter assays showed that miRNA-574-5p was a target of NALT1. Additionally, dual-luciferase reporter assays, Ago2-RIP, and rescue experiments indicated that miRNA-574-5p could target the PEG10 gene directly. Our results suggested that NALT1 promoted CRC proliferation and migration by sponging miRNA-574-5p to upregulate PEG10 expression, and implied that NALT1 might act as a promising biomarker and therapeutic target for CRC.
The long noncoding RNA TINCR promotes self-renewal of human liver cancer stem cells through autophagy activation
Authors: Shi Jing , Guo Cao , Li Yang , Ma Junli 
Published: November 2022

AbstractHepatocellular carcinoma (HCC) is an extraordinarily heterogeneous tumor, which holds high recurrence and metastasis rates. Liver cancer stem cells (LCSCs) have been considered to be important influencing factors of these pathological properties, but the underlying mechanisms are poorly understood in HCC. Considerable evidences have shown that autophagy has an important role in cancer stemness. However, it is still unknown whether a long noncoding RNA (lncRNA) TINCR is involved in autophagy and self-renewal maintenance of HCC. In this study, TINCR was found to be highly expressed in HCC tissues and LCSCs. In vitro and in vivo assays for the first time showed that TINCR was required for LCSC self-renewal and tumorigenesis. Moreover, gene ontology analysis revealed the involvement of autophagy in the maintenance of TINCR-regulated stemness. Mechanically, TINCR was associated with polypyrimidine tract binding protein 1 (PTBP1) protein, which further promoted the transcription activity of autophagy related gene ATG5. In conclusion, we demonstrated that TINCR regulated LCSC self-renewal by autophagy activation through PTBP1/ATG5 regulatory pathway, offering a potential new target for HCC therapy.
Crystal growth in confinement
Authors: Kohler Felix , Pierre-Louis Olivier , Dysthe Dag Kristian 
Published: November 2022

AbstractThe growth of crystals confined in porous or cellular materials is ubiquitous in Nature and forms the basis of many industrial processes. Confinement affects the formation of biominerals in living organisms, of minerals in the Earth’s crust and of salt crystals damaging porous limestone monuments, and is also used to control the growth of artificial crystals. However, the mechanisms by which confinement alters crystal shapes and growth rates are still not elucidated. Based on novel in situ optical observations of (001) surfaces of NaClO3 and CaCO3 crystals at nanometric distances from a glass substrate, we demonstrate that new molecular layers can nucleate homogeneously and propagate without interruption even when in contact with other solids, raising the macroscopic crystal above them. Confined growth is governed by the peculiar dynamics of these molecular layers controlled by the two-dimensional transport of mass through the liquid film from the edges to the center of the contact, with distinctive features such as skewed dislocation spirals, kinetic localization of nucleation in the vicinity of the contact edge, and directed instabilities. Confined growth morphologies can be predicted from the values of three main dimensionless parameters.
Intensive grassland management disrupts below-ground multi-trophic resource transfer in response to drought
Authors: Chomel Mathilde , Lavallee Jocelyn M. , Alvarez-Segura Nil , Baggs Elizabeth M. , Caruso Tancredi , de Castro Francisco , Emmerson Mark C. , Magilton Matthew , Rhymes Jennifer M. , de Vries Franciska T. , Johnson David , Bardgett Richard D. 
Published: November 2022

AbstractModification of soil food webs by land management may alter the response of ecosystem processes to climate extremes, but empirical support is limited and the mechanisms involved remain unclear. Here we quantify how grassland management modifies the transfer of recent photosynthates and soil nitrogen through plants and soil food webs during a post-drought period in a controlled field experiment, using in situ 13C and 15N pulse-labelling in intensively and extensively managed fields. We show that intensive management decrease plant carbon (C) capture and its transfer through components of food webs and soil respiration compared to extensive management. We observe a legacy effect of drought on C transfer pathways mainly in intensively managed grasslands, by increasing plant C assimilation and 13C released as soil CO2 efflux but decreasing its transfer to roots, bacteria and Collembola. Our work provides insight into the interactive effects of grassland management and drought on C transfer pathways, and highlights that capture and rapid transfer of photosynthates through multi-trophic networks are key for maintaining grassland resistance to drought.
Compensatory epistasis maintains ACE2 affinity in SARS-CoV-2 Omicron BA.1
Authors: Moulana Alief , Dupic Thomas , Phillips Angela M. , Chang Jeffrey , Nieves Serafina , Roffler Anne A. , Greaney Allison J. , Starr Tyler N. , Bloom Jesse D. , Desai Michael M. 
Published: November 2022

AbstractThe Omicron BA.1 variant emerged in late 2021 and quickly spread across the world. Compared to the earlier SARS-CoV-2 variants, BA.1 has many mutations, some of which are known to enable antibody escape. Many of these antibody-escape mutations individually decrease the spike receptor-binding domain (RBD) affinity for ACE2, but BA.1 still binds ACE2 with high affinity. The fitness and evolution of the BA.1 lineage is therefore driven by the combined effects of numerous mutations. Here, we systematically map the epistatic interactions between the 15 mutations in the RBD of BA.1 relative to the Wuhan Hu-1 strain. Specifically, we measure the ACE2 affinity of all possible combinations of these 15 mutations (215 = 32,768 genotypes), spanning all possible evolutionary intermediates from the ancestral Wuhan Hu-1 strain to BA.1. We find that immune escape mutations in BA.1 individually reduce ACE2 affinity but are compensated by epistatic interactions with other affinity-enhancing mutations, including Q498R and N501Y. Thus, the ability of BA.1 to evade immunity while maintaining ACE2 affinity is contingent on acquiring multiple interacting mutations. Our results implicate compensatory epistasis as a key factor driving substantial evolutionary change for SARS-CoV-2 and are consistent with Omicron BA.1 arising from a chronic infection.
Increased slow dynamics defines ligandability of BTB domains
Authors: Kharchenko Vladlena , Linhares Brian M. , Borregard Megan , Czaban Iwona , Grembecka Jolanta , Jaremko Mariusz , Cierpicki Tomasz , Jaremko Łukasz 
Published: November 2022

AbstractEfficient determination of protein ligandability, or the propensity to bind small-molecules, would greatly facilitate drug development for novel targets. Ligandability is currently assessed using computational methods that typically consider the static structural properties of putative binding sites or by experimental fragment screening. Here, we evaluate ligandability of conserved BTB domains from the cancer-relevant proteins LRF, KAISO, and MIZ1. Using fragment screening, we discover that MIZ1 binds multiple ligands. However, no ligands are uncovered for the structurally related KAISO or LRF. To understand the principles governing ligand-binding by BTB domains, we perform comprehensive NMR-based dynamics studies and find that only the MIZ1 BTB domain exhibits backbone µs-ms time scale motions. Interestingly, residues with elevated dynamics correspond to the binding site of fragment hits and recently defined HUWE1 interaction site. Our data argue that examining protein dynamics using NMR can contribute to identification of cryptic binding sites, and may support prediction of the ligandability of novel challenging targets.
Covalent transfer of chemical gradients onto a graphenic surface with 2D and 3D control
Authors: Xia Yuanzhi , Sevim Semih , Vale João Pedro , Seibel Johannes , Rodríguez-San-Miguel David , Kim Donghoon , Pané Salvador , Mayor Tiago Sotto , De Feyter Steven , Puigmartí-Luis Josep 
Published: November 2022

AbstractControl over the functionalization of graphenic materials is key to enable their full application in electronic and optical technologies. Covalent functionalization strategies have been proposed as an approach to tailor the interfaces’ structure and properties. However, to date, none of the proposed methods allow for a covalent functionalization with control over the grafting density, layer thickness and/or morphology, which are key aspects for fine-tuning the processability and performance of graphenic materials. Here, we show that the no-slip boundary condition at the walls of a continuous flow microfluidic device offers a way to generate controlled chemical gradients onto a graphenic material with 2D and 3D control, a possibility that will allow the sophisticated functionalization of these technologically-relevant materials.
Regulating electron configuration of single Cu sites via unsaturated N,O-coordination for selective oxidation of benzene
Authors: Zhang Ting , Sun Zhe , Li Shiyan , Wang Baojun , Liu Yuefeng , Zhang Riguang , Zhao Zhongkui 
Published: November 2022

AbstractDeveloping highly efficient catalyst for selective oxidation of benzene to phenol (SOBP) with low H2O2consumption is highly desirable for practical application, but challenge remains. Herein, we report unique single-atom Cu1-N1O2coordination-structure on N/C material (Cu-N1O2SA/CN), prepared by water molecule-mediated pre-assembly-pyrolysis method, can efficiently boost SOBP reaction at a 2:1 of low H2O2/benzene molar ratio, showing 83.7% of high benzene conversion with 98.1% of phenol selectivity. The Cu1-N1O2sites can provide a preponderant reaction pathway for SOBP reaction with less steps and lower energy barrier. As a result, it shows an unexpectedly higher turnover frequency (435 h−1) than that of Cu1-N2(190 h−1), Cu1-N3(90 h−1) and Cu nanoparticle (58 h−1) catalysts, respectively. This work provides a facile and efficient method for regulating the electron configuration of single-atom catalyst and generates a highly active and selective non-precious metal catalyst for industrial production of phenol through selective oxidation of benzene.
Improved finite element method for flow, heat and solute transport of Prandtl liquid via heated plate
Authors: Hafeez Muhammad Bilal , Krawczuk Marek , Jamshed Wasim , Kaneez Hajra , Hussain Syed M. , El Din El Sayed M. Tag 
Published: November 2022

AbstractIn the current study, a vertical, 3D-heated plate is used to replicate the generation of heat energy and concentration into Prandtl liquid. We discuss how Dufour and Soret theories relate to the equations for concentration and energy. In order to see how effectively particles, interact with heat and a solvent, hybrid nanoparticles are used. It does away with the phenomena of viscous dissipation and changing magnetic fields. The motivation behind the developed study is to optimize solvent and heat storage uses in the biological and industrial domains. This article's major goal is to explore the aspects of thermal energy and mass transfer that influence how nanoparticles, hybrid nanoparticles, and 3D melting surface sheets behave. Variable thermal efficiency and variable mass transfer are combined. The system of generated PDEs (difference equations) includes the concentration, velocity, and heat energy equations. The numerical calculations are done for Silver (Ag), Molybdenum Disulfide (MoS2) nanoparticles with Ethylene glycol (C2H6O2) as the base fluid using a boundary layer approach to the mathematical formulation. The system of ODEs is formulated through transformations in order to find a solution. A Galerkin finite element algorithm (G-FEA) is adopted to analyze various aspects versus different parameters. It has been found that motion into hybrid nanoparticles is reduced by motion into nanoparticles. Additionally, differences in heat energy and solvent particle sizes are associated with modifications in magnetic, Dufour, Eckert, and Soret numbers. In contrast to hybrid nanostructures, the output of thermal energy is usually observed to be substantially higher. The magnetic field parameter decreases the particle velocity. In contradiction to the Eckert number, bouncy parameter, and magnetic parameter set values, the maximum quantity of heat energy is obtained. variable thermal conductivity's function. The 3D heated vertical surface convective heat transfer of nanofluids and hybrid nanofluids under the impact of a heat source, thermal radiation, and viscous dissipation has not yet been studied, as far as the authors are aware.
Genomic and ecological evidence shed light on the recent demographic history of two related invasive insects
Authors: Poveda-Martínez Daniel , Salinas Nicolas A. , Aguirre María Belén , Sánchez-Restrepo Andrés F. , Hight Stephen , Díaz-Soltero Hilda , Logarzo Guillermo , Hasson Esteban 
Published: November 2022

AbstractHypogeococcus pungens is a species complex native to southern South America that is composed of at least five putative species, each one specialized in the use of different host plants. Two of these undescribed species were registered as invasive in Central and North America: Hyp-C is a cactophagous mealybug that became an important pest that threatens endemic cactus species in Puerto Rico, and Hyp-AP feeds on Amaranthaceae and Portulacaceae hosts, but does not produce severe damage to the host plants. We quantified genomic variation and investigated the demographic history of both invasive species by means of coalescent-based simulations using high throughput sequencing data. We also evaluated the incidence of host plant infestation produced by both species and used an ecological niche modeling approach to assess potential distribution under current and future climatic scenarios. Our genetic survey evinced the footprints of strong effective population size reduction and signals of genetic differentiation among populations within each species. Incidence of plant attacks varied between species and among populations within species, with some host plant species preferred over others. Ecological niche modeling suggested that under future climatic scenarios both species would expand their distribution ranges in Puerto Rico. These results provide valuable information for the design of efficient management and control strategies of the Puerto Rican cactus pest and shed light on the evolutionary pathways of biological invasions.
Analysis on ecological characteristics of Mississippian coral reefs in Langping, Guangxi
Authors: Yang Dayong , Chang Honglun , Liu Xiao , Wan Peng , Shen Liming 
Published: November 2022

AbstractSeveral Late Viséan-Serpukhovian coral reefs were identified in Langping, Tianlin. They provided an opportunity to investigate paleo-environments suitable for the development of reef-building communities and the construction of coral reefs in Langping. In this paper, part of the reef-building environmental and the ecological characteristics of coral reefs then were elaborated by analyzing the development settings, palaeogeography, sedimentation of reefs, the response to hydrodynamic conditions of reef-building corals, effects of disturbance and non-reef-building organism on reef communities, and the influence of coral morphology on reef development. It is considered that the sedimentary environment of Langping in Late Viséan-Serpukhovian is suitable for the development of benthic communities. The current appearance of reefs is determined by both coral populations ecological characteristics and reef-building environment.
Influences of sleep and lifestyle factors on the risk for covid-19 infections, from internet survey of 10,000 Japanese business workers
Authors: Nakashima Masahiro , Amano Ryota , Nishino Naoya , Osada Yasutaka , Watanabe Yuriko , Miyake Akifumi , Chiba Shintaro , Nishino Seiji 
Published: November 2022

AbstractWe conducted an internet survey to assess sociodemographic variables, lifestyle factors, sleep problems, and comorbidities for sleep apnea syndrome (SAS) in COVID-19 and influenza (FLU) infections. Data from 10,323 workers (50.0% male) were analyzed. COVID-19 was diagnosed in 144 subjects (COVID-19+), and 8,693 were classified as not suspected to be infected (COVID-19−). SAS had been diagnosed in 35.4% of the COVID-19+ subjects, but only 231 (2.7%) of the 8,693 COVID-19− subjects. COVID-19+ subjects were more susceptible to FLU (35.4%) compared to COVID-19− subjects (3.0%). A multivariate analysis revealed that higher risks of COVID-19+ were linked to the following factors: going out without a face mask (OR 7.05, 95% CI 4.53–11.00), FLU+ (OR 6.33, 95% CI 3.80–10.54), excessive exercise before going to sleep (OR 2.10, 95% CI 1.63–2.70), SAS+ (OR 5.08, 95% CI 2.88–8.94), younger age (OR 1.05, 95% CI 1.03–1.07), falling sleep while sitting or talking with someone (OR 3.70, 95% CI 2.30–5.95), and use of hypnotics (OR 2.28, 95% CI 1.20–4.30). Since sleep impairment played a relatively small role in COVID-19+/SAS− subjects, we assume that SAS itself was a more significant risk factor for COVID-19 infection rather than sleep impairment. A better understanding of the mechanisms that result in increased susceptibility to COVID-19 in SAS is vital for helping prevent COVID-19.
Effect of marigold (Tagetes erecta L.) on soil microbial communities in continuously cropped tobacco fields
Authors: Huang Feiyan , Deng Xiaopeng , Gao Lingling , Cai Xianjie , Yan Ding , Cai Yongzhan , Chen Xiaolong , Yang Min , Tong Wenjie , Yu Lei 
Published: November 2022

AbstractRoot-knot nematode disease is a catastrophic soil-borne disease in tobacco production. The regulation of natural microbial communities is considered a good disease management approach to suppress the incidence of soilborne diseases. In this study, the effects of tobacco (Nicotiana tabacum L.)-marigold (Tagetes erecta L.) rotation on the diversity and structure of soil microbial communities in continuously cropped tobacco fields were analyzed to manage this devastating pathogen. The results showed that the soil bacterial OTUs increased after marigold rotation and that the bacterial Shannon, ACE, Chao1 index, and fungal Shannon index were higher in the tobacco-marigold rotation fields than in the continuously cropped tobacco fields by 3.98%, 10.37%, 5.46%, and 3.43%, respectively. After marigold rotation, the relative abundances of Actinobacteria, Acidobacteria, and Ascomycota increased by 28.62%, 107.50%, and 57.44%, respectively, and the proportion of beneficial bacterial genera such as Nocardioides, Gemmatimonas, and Bradyrhizobium increased. In addition, our results also showed that rotation of marigold could effectively reduce the incidence of root-knot nematodes in the next crop of tobacco. These results indicate that marigold rotation had a positive effect on the soil microecological environment of continuously cropped tobacco fields, reducing the obstacles to continuous cropping of tobacco.
Modulating the poly-l-lysine structure through the control of the protonation–deprotonation state of l-lysine
Authors: Stagi Luigi , Sini Martina , Carboni Davide , Anedda Roberto , Siligardi Giuliano , Gianga Tiberiu-Marius , Hussain Rohanah , Innocenzi Plinio 
Published: November 2022

AbstractDesigning the architecture of l-lysine-based polymeric structures is a highly challenging task that requires careful control of the amino acid reactive groups. Conventional processes to obtain branched polylysine need several steps and the addition of specific catalysts. In the present work, to gain a better understanding and control of the formation of l-lysine-based polymers, we have investigated the correlation between the protonation state of l-lysine and the corresponding hydrothermally grown structures. The samples have been characterized by combining optical spectroscopies, such as UV–Vis, fluorescence, and synchrotron radiation circular dichroism with structural analysis by Nuclear Magnetic Resonance, Fourier Transform Infrared spectroscopy, and dynamic light scattering. We have observed that aqueous precursor solutions with alkaline pHs promote the formation of branched structures. In contrast, high pHs favour the reactivity of the ε-amino groups leading to linear structures, as shown by circular dichroism analyses. On the other hand, acidic conditions trigger the branching of the amino acid. Interestingly, the polymeric forms of l-lysine emit in the blue because the increasing number of intermolecular hydrogen bonds promote the intermolecular charge transfer responsible for the emission. Understanding the correlation between the l-lysine charged states and the polymeric structures that could form controlling the protonation–deprotonation states of the amino acid opens the route to a refined design of polypeptide systems based on l-lysine.