bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations
Authors: Conrad Roth E , Viver Tomeu , Gago Juan F , Hatt Janet K , Venter Stephanus N , Rossello-Mora Ramon , Konstantinidis Konstantinos T 
Published: December 2021

AbstractMetagenomic surveys have revealed that natural microbial communities are predominantly composed of sequence-discrete, species-like populations but the genetic and/or ecological processes that maintain such populations remain speculative, limiting our understanding of population speciation and adaptation to perturbations. To address this knowledge gap, we sequenced 112 Salinibacter ruber isolates and 12 companion metagenomes from four adjacent saltern ponds in Mallorca, Spain that were experimentally manipulated to dramatically alter salinity and light intensity, the two major drivers of this ecosystem. Our analyses showed that the pangenome of the local Sal. ruber population is open and similar in size (~15,000 genes) to that of randomly sampled Escherichia coli genomes. While most of the accessory (noncore) genes were isolate-specific and showed low in situ abundances based on the metagenomes compared to the core genes, indicating that they were functionally unimportant and/or transient, 3.5% of them became abundant when salinity (but not light) conditions changed and encoded for functions related to osmoregulation. Nonetheless, the ecological advantage of these genes, while significant, was apparently not strong enough to purge diversity within the population. Collectively, our results provide an explanation for how this immense intrapopulation gene diversity is maintained, which has implications for the prokaryotic species concept.
Protozoa populations are ecosystem engineers that shape prokaryotic community structure and function of the rumen microbial ecosystem
Authors: Solomon Ronnie , Wein Tanita , Levy Bar , Eshed Shahar , Dror Rotem , Reiss Veronica , Zehavi Tamar , Furman Ori , Mizrahi Itzhak , Jami Elie 
Published: December 2021

Abstract
Unicellular eukaryotes are an integral part of many microbial ecosystems where they interact with their surrounding prokaryotic community—either as predators or as mutualists. Within the rumen, one of the most complex host-associated microbial habitats, ciliate protozoa represent the main micro-eukaryotes, accounting for up to 50% of the microbial biomass. Nonetheless, the extent of the ecological effect of protozoa on the microbial community and on the rumen metabolic output remains largely understudied. To assess the role of protozoa on the rumen ecosystem, we established an in-vitro system in which distinct protozoa sub-communities were introduced to the native rumen prokaryotic community. We show that the different protozoa communities exert a strong and differential impact on the composition of the prokaryotic community, as well as its function including methane production. Furthermore, the presence of protozoa increases prokaryotic diversity with a differential effect on specific bacterial populations such as Gammaproteobacteria, Prevotella and Treponema. Our results suggest that protozoa contribute to the maintenance of prokaryotic diversity in the rumen possibly by mitigating the effect of competitive exclusion between bacterial taxa. Our findings put forward the rumen protozoa populations as potentially important ecosystem engineers for future microbiome modulation strategies.
Mitochondrial DNA leakage exacerbates odontoblast inflammation through gasdermin D-mediated pyroptosis
Authors: Zhang Yi-Fei , Zhou Lu , Mao Han-Qing , Yang Fu-Hua , Chen Zhi , Zhang Lu 
Published: December 2021

AbstractAlleviating odontoblast inflammation is crucial to control the progression of pulpitis. Mitochondrial DNA (mtDNA) is a vital driver of inflammation when it leaks from mitochondria of inflamed odontoblasts into the cytosol. Bacteria-induced inflammation leads to a novel type of cell death named pyroptosis. The canonical pyroptosis is a gasdermin (GSDM)-dependent cytolytic programmed cell death characterized by cell swelling and pore formation in the plasma membrane. To date, whether odontoblast cytosolic mtDNA regulates dental pulp inflammation through the canonical pyroptosis pathway remains to be elucidated. In this study, high gasdermin D (GSDMD) expression was detected in human pulpitis. We found that LPS stimulation of mDPC6T cells promoted BAX translocation from the cytosol to the mitochondrial membrane, leading to mtDNA release. Moreover, overexpression of isolated mtDNA induced death in a large number of mDPC6T cells, which had the typical appearance of pyroptotic cells. Secretion of the inflammatory cytokines CXCL10 and IFN-β was also induced by mtDNA. These results suggest that cytosolic mtDNA participates in the regulation of odontoblast inflammation through GSDMD-mediated pyroptosis in vitro. Interestingly, after overexpression of mtDNA, the expression of inflammatory cytokines CXCL10 and IFN-β was increased and not decreased in GSDMD knockdown mDPC6T cells. We further proposed a novel model in which STING-dependent inflammation in odontoblast-like cell is a compensatory mechanism to control GSDMD-mediated pyroptosis, jointly promoting the immune inflammatory response of odontoblasts. Collectively, these findings provide the first demonstration of the role of the mtDNA-GSDMD-STING in controlling odontoblast inflammation and a detailed description of the underlying interconnected relationship.
Loss-of-function alleles of ZmPLD3 cause haploid induction in maize
Authors: Li Yuan , Lin Zhen , Yue Yang , Zhao Haiming , Fei Xiaohong , E. Lizhu , Liu Chenxu , Chen Shaojiang , Lai Jinsheng , Song Weibin 
Published: December 2021

AbstractDoubled haploid technology has been widely applied to multiple plant species and is recognized as one of the most important technologies for improving crop breeding efficiency. Although mutations in MATRILINEAL/Zea mays PHOSPHOLIPASE A1/NOT LIKE DAD (MTL/ZmPLA1/NLD) and Zea mays DOMAIN OF UNKNOWN FUNCTION 679 MEMBRANE PROTEIN (ZmDMP) have been shown to generate haploids in maize, knowledge of the genetic basis of haploid induction (HI) remains incomplete. Therefore, cloning of new genes underlying HI is important for further elucidating its genetic architecture. Here, we found that loss-of-function mutations of Zea mays PHOSPHOLIPASE D3 (ZmPLD3), one of the members from the phospholipase D subfamily, could trigger maternal HI in maize. ZmPLD3 was identified through a reverse genetic strategy based on analysis of pollen-specifically expressed phospholipases, followed by validation through the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9 (CRISPR–Cas9) system. Mutations of ZmPLD3 resulted in a haploid induction rate (HIR) similar to that of mtl/zmpla1/nld and showed synergistic effects rather than functional redundancy on tripling the HIR (from 1.19% to 4.13%) in the presence of mtl/zmpla1/nld. RNA-seq profiling of mature pollen indicated that a large number of pollen-specific differentially expressed genes were enriched in processes related to gametogenesis development, such as pollen tube development and cell communication, during the double-fertilization process. In addition, ZmPLD3 is highly conserved among cereals, highlighting the potential application of these in vivo haploid-inducer lines for other important crop plant species. Collectively, our discovery identifies a novel gene underlying in vivo maternal HI and provides possibility of breeding haploid inducers with further improved HIR.
Inverse design of two-dimensional materials with invertible neural networks
Authors: Fung Victor , Zhang Jiaxin , Hu Guoxiang , Ganesh P. , Sumpter Bobby G. 
Published: December 2021

AbstractThe ability to readily design novel materials with chosen functional properties on-demand represents a next frontier in materials discovery. However, thoroughly and efficiently sampling the entire design space in a computationally tractable manner remains a highly challenging task. To tackle this problem, we propose an inverse design framework (MatDesINNe) utilizing invertible neural networks which can map both forward and reverse processes between the design space and target property. This approach can be used to generate materials candidates for a designated property, thereby satisfying the highly sought-after goal of inverse design. We then apply this framework to the task of band gap engineering in two-dimensional materials, starting with MoS2. Within the design space encompassing six degrees of freedom in applied tensile, compressive and shear strain plus an external electric field, we show the framework can generate novel, high fidelity, and diverse candidates with near-chemical accuracy. We extend this generative capability further to provide insights regarding metal-insulator transition in MoS2 which are important for memristive neuromorphic applications, among others. This approach is general and can be directly extended to other materials and their corresponding design spaces and target properties.
Probable detection of an eruptive filament from a superflare on a solar-type star
Authors: Namekata Kosuke , Maehara Hiroyuki , Honda Satoshi , Notsu Yuta , Okamoto Soshi , Takahashi Jun , Takayama Masaki , Ohshima Tomohito , Saito Tomoki , Katoh Noriyuki , Tozuka Miyako , Murata Katsuhiro L. , Ogawa Futa , Niwano Masafumi , Adachi Ryo , Oeda Motoki , Shiraishi Kazuki , Isogai Keisuke , Seki Daikichi , Ishii Takako T. , Ichimoto Kiyoshi , Nogami Daisaku , Shibata Kazunari 
Published: December 2021

AbstractSolar flares are often accompanied by filament/prominence eruptions (~104 K and ~1010−11 cm−3), sometimes leading to coronal mass ejections that directly affect the Earth’s environment1,2. ‘Superflares’ are found on some active solar-type (G-type main-sequence) stars3–5, but the filament eruption–coronal mass ejection association has not been established. Here we show that our optical spectroscopic observation of the young solar-type star EK Draconis reveals evidence for a stellar filament eruption associated with a superflare. This superflare emitted a radiated energy of 2.0 × 1033 erg, and a blueshifted hydrogen absorption component with a high velocity of −510 km s−1 was observed shortly afterwards. The temporal changes in the spectra strongly resemble those of solar filament eruptions. Comparing this eruption with solar filament eruptions in terms of the length scale and velocity strongly suggests that a stellar coronal mass ejection occurred. The erupted filament mass of 1.1 × 1018 g is ten times larger than those of the largest solar coronal mass ejections. The massive filament eruption and an associated coronal mass ejection provide the opportunity to evaluate how they affect the environment of young exoplanets/the young Earth6 and stellar mass/angular momentum evolution7.
Correlating biological activity to thermo-structural analysis of the interaction of CTX with synthetic models of macrophage membranes
Authors: de Araújo Pimenta Luciana , Duarte Evandro L. , Muniz Gabriel S. Vignoli , Pasqualoto Kerly Fernanda Mesquita , de Mattos Fontes Marcos Roberto , Lamy M. Teresa , Sampaio Sandra Coccuzzo 
Published: December 2021

AbstractThe important pharmacological actions of Crotoxin (CTX) on macrophages, the main toxin in the venom of Crotalus durissus terrificus, and its important participation in the control of different pathophysiological processes, have been demonstrated. The biological activities performed by macrophages are related to signaling mediated by receptors expressed on the membrane surface of these cells or opening and closing of ion channels, generation of membrane curvature and pore formation. In the present work, the interaction of the CTX complex with the cell membrane of macrophages is studied, both using biological cells and synthetic lipid membranes to monitor structural alterations induced by the protein. Here we show that CTX can penetrate THP-1 cells and induce pores only in anionic lipid model membranes, suggesting that a possible access pathway for CTX to the cell is via lipids with anionic polar heads. Considering that the selectivity of the lipid composition varies in different tissues and organs of the human body, the thermostructural studies presented here are extremely important to open new investigations on the biological activities of CTX in different biological systems.
Effect of human secretory calcium-binding phosphoprotein proline-glutamine rich 1 protein on Porphyromonas gingivalis and identification of its active portions
Authors: Mary Charline , Fouillen Aurélien , Moffatt Pierre , Guadarrama Bello Dainelys , Wazen Rima M. , Grenier Daniel , Nanci Antonio 
Published: December 2021

AbstractThe mouth environment comprises the second most significant microbiome in the body, and its equilibrium is critical in oral health. Secretory calcium-binding phosphoprotein proline-glutamine rich 1 (SCPPPQ1), a protein normally produced by the gingival epithelium to mediate its attachment to teeth, was suggested to be bactericidal. Our aim was to further explore the antibacterial potential of human SCPPPQ1 by characterizing its mode of action and identifying its active portions. In silico analysis showed that it has molecular parallels with antimicrobial peptides. Incubation of Porphyromonasgingivalis, a major periodontopathogen, with the full-length protein resulted in decrease in bacterial number, formation of aggregates and membrane disruptions. Analysis of SCPPPQ1-derived peptides indicated that these effects are sustained by specific regions of the molecule. Altogether, these data suggest that human SCPPPQ1 exhibits antibacterial capacity and provide new insight into its mechanism of action.
Spreading of disturbances in realistic models of transmission grids in dependence on topology, inertia and heterogeneity
Authors: Nnoli Kosisochukwu P. , Kettemann Stefan 
Published: December 2021

AbstractThe energy transition towards more renewable energy resources (RER) profoundly affects the frequency dynamics and stability of electrical power networks. Here, we investigate systematically the effect of reduced grid inertia, due to an increase in the magnitude of RER, its heterogeneous distribution and the grid topology on the propagation of disturbances in realistic power grid models. These studies are conducted with the DigSILENT PowerFactory software. By changing the power generation at one central bus in each grid at a specific time, we record the resulting frequency transients at all buses. Plotting the time of arrival (ToA) of the disturbance at each bus versus the distance from the disturbance, we analyse its propagation throughout the grid. While the ToAs are found to be distributed, we confirm a tendency that the ToA increases with geodesic distance linearly. Thereby, we can measure an average velocity of propagation by fitting the data with a ballistic equation. This velocity is found to decay with increasing inertia. Characterising each grid by its meshedness coefficient, we find that the distribution of the ToAs depends in more meshed grids less strongly on the grid inertia. In order to take into account the inhomogeneous distribution of inertia, we introduce an effective distance$$r_{\mathrm{eff}}$$reff, which is weighted with a factor which strongly depends on local inertia. We find that this effective distance is more strongly correlated with the ToAs, for all grids. This is confirmed quantitatively by obtaining a larger Pearson correlation coefficient between ToA and$$r_{\mathrm{eff}}$$reffthan withr. Remarkably, a ballistic equation for the ToA with a velocity, as derived from the swing equation, provides a strict lower bound for all effective distances$$r_{\mathrm{eff}}$$reffin all power grids. thereby yielding a reliable estimate for the smallest time a disturbance needs to propagate that distance as function of system parameters, in particular inertia. We thereby conclude that in the analysis of contingencies of power grids it may be advisable that system designers and operators use the effective distance$$r_{\mathrm{eff}}$$reff, taking into account inhomogeneous distribution of inertia as introduced in Eq. (12), to locate a disturbance. Moreover, our results provide evidence for the importance of the network topology as quantified by the meshedness coefficient$$\beta$$β.
Characterization of recombinant β subunit of human MUC4 mucin (rMUC4β)
Authors: Kshirsagar Prakash G. , Gulati Mansi , Junker Wade M. , Aithal Abhijit , Spagnol Gaelle , Das Srustidhar , Mallya Kavita , Gautam Shailendra K. , Kumar Sushil , Sorgen Paul , Pandey Krishan K. , Batra Surinder K. , Jain Maneesh 
Published: December 2021

AbstractMUC4 is a transmembrane mucin expressed on various epithelial surfaces, including respiratory and gastrointestinal tracts, and helps in their lubrication and protection. MUC4 is also aberrantly overexpressed in various epithelial malignancies and functionally contributes to cancer development and progression. MUC4 is putatively cleaved at the GDPH site into a mucin-like α-subunit and a membrane-tethered growth factor-like β-subunit. Due to the presence of several functional domains, the characterization of MUC4β is critical for understanding MUC4 biology. We developed a method to produce and purify multi-milligram amounts of recombinant MUC4β (rMUC4β). Purified rMUC4β was characterized by Far-UV CD and I-TASSER-based protein structure prediction analyses, and its ability to interact with cellular proteins was determined by the affinity pull-down assay. Two of the three EGF-like domains exhibited typical β-fold, while the third EGF-like domain and vWD domain were predominantly random coils. We observed that rMUC4β physically interacts with Ezrin and EGFR family members. Overall, this study describes an efficient and simple strategy for the purification of biologically-active rMUC4β that can serve as a valuable reagent for a variety of biochemical and functional studies to elucidate MUC4 function and generating domain-specific antibodies and vaccines for cancer immunotherapy.
Volatile organic compounds as a potential screening tool for neoplasm of the digestive system: a meta-analysis
Authors: Wang Lixing , Li Junan , Xiong Xiaoliang , Hao Tingting , Zhang Chao , Gao Zhao , Zhong Lili , Zhao Yinlong 
Published: December 2021

AbstractThis meta-analysis was aimed to estimate the diagnostic performance of volatile organic compounds (VOCs) as a potential novel tool to screen for the neoplasm of the digestive system. An integrated literature search was performed by two independent investigators to identify all relevant studies investigating VOCs in diagnosing neoplasm of the digestive system from inception to 7th December 2020. STATA and Revman software were used for data analysis. The methodological quality of each study was assessed using the Quality Assessment of Diagnostic Accuracy Studies tool. A bivariate mixed model was used and meta-regression and subgroup analysis were performed to identify possible sources of heterogeneity. A total of 36 studies comprised of 1712 cases of neoplasm and 3215 controls were included in our meta-analysis. Bivariate analysis showed a pooled sensitivity of 0.87 (95% confidence interval (CI) 0.83–0.90), specificity of 0.86 (95% CI 0.82–0.89), a positive likelihood ratio of 6.18 (95% CI 4.68–8.17), and a negative likelihood ratio of 0.15 (95% CI 0.12–0.20). The diagnostic odds ratio and the area under the summary ROC curve for diagnosing neoplasm of the digestive system were 40.61 (95% CI 24.77–66.57) and 0.93 (95% CI 0.90–0.95), respectively. Our analyses revealed that VOCs analysis could be considered as a potential novel tool to screen for malignant diseases of the digestive system.
Entropy generation and induced magnetic field in pseudoplastic nanofluid flow near a stagnant point
Authors: Hou Enran , Hussain Azad , Rehman Aysha , Baleanu Dumitru , Nadeem Sohail , Matoog R. T. , Khan Ilyas , Sherif El-Sayed M. 
Published: December 2021

AbstractIn this present article the entropy generation, induced magnetic field, and mixed convection stagnant point flow of pseudoplastic nano liquid over an elastic surface is investigated. The Buongiorno model is employed in modeling. Through the use of the boundary layer idea, flow equations are transformed from compact to component form. The system of equations is solved numerically. The Induced magnetic spectrum falls near the boundary and grows further away as the reciprocal of the magnetic Prandtl number improves. The fluctuation of induced magnetic rises while expanding the values of mixed convection, thermophoresis, and magnetic parameters, whereas it declines for increment in the Brownian and stretching parameters. The velocity amplitude ascends and temperature descends for the rise in magnetic parameter. The mass transfer patterns degrade for the higher amount of buoyancy ratio while it boosts by the magnification of mixed convection and stretching parameters. Streamlines behavior is also taken into account against the different amounts of mixed convection and magnetic parameters. The pseudoplastic nanofluids are applicable in all electronic devices for increasing the heating or cooling rate in them. Further, pseudoplastic nanofluids are also applicable in reducing skin friction coefficient.
Preclinical evidence of remote ischemic conditioning in ischemic stroke, a metanalysis update
Authors: Torres-Querol Coral , Quintana-Luque Manuel , Arque Gloria , Purroy Francisco 
Published: December 2021

AbstractRemote ischemic conditioning (RIC) is a promising therapeutic approach for ischemic stroke patients. It has been proven that RIC reduces infarct size and improves functional outcomes. RIC can be applied either before ischemia (pre-conditioning; RIPreC), during ischemia (per-conditioning; RIPerC) or after ischemia (post-conditioning; RIPostC). Our aim was to systematically determine the efficacy of RIC in reducing infarct volumes and define the cellular pathways involved in preclinical animal models of ischemic stroke. A systematic search in three databases yielded 50 peer-review articles. Data were analyzed using random effects models and results expressed as percentage of reduction in infarct size (95% CI). A meta-regression was also performed to evaluate the effects of covariates on the pooled effect-size. 95.3% of analyzed experiments were carried out in rodents. Thirty-nine out of the 64 experiments studied RIPostC (61%), sixteen examined RIPreC (25%) and nine tested RIPerC (14%). In all studies, RIC was shown to reduce infarct volume (− 38.36%; CI − 42.09 to − 34.62%) when compared to controls. There was a significant interaction caused by species. Short cycles in mice significantly reduces infarct volume while in rats the opposite occurs. RIPreC was shown to be the most effective strategy in mice. The present meta-analysis suggests that RIC is more efficient in transient ischemia, using a smaller number of RIC cycles, applying larger length of limb occlusion, and employing barbiturates anesthetics. There is a preclinical evidence for RIC, it is safe and effective. However, the exact cellular pathways and underlying mechanisms are still not fully determined, and its definition will be crucial for the understanding of RIC mechanism of action.