bluuebunny/crossref_metadata_2025_split huggingface dataset:
The occurrence and ecology of microbial chain elongation of carboxylates in soils
Authors: Joshi Sayalee , Robles Aide , Aguiar Samuel , Delgado Anca G 
Published: February 2021

Abstract
Chain elongation is a growth-dependent anaerobic metabolism that combines acetate and ethanol into butyrate, hexanoate, and octanoate. While the model microorganism for chain elongation, Clostridium kluyveri, was isolated from a saturated soil sample in the 1940s, chain elongation has remained unexplored in soil environments. During soil fermentative events, simple carboxylates and alcohols can transiently accumulate up to low mM concentrations, suggesting in situ possibility of microbial chain elongation. Here, we examined the occurrence and microbial ecology of chain elongation in four soil types in microcosms and enrichments amended with chain elongation substrates. All soils showed evidence of chain elongation activity with several days of incubation at high (100 mM) and environmentally relevant (2.5 mM) concentrations of acetate and ethanol. Three soils showed substantial activity in soil microcosms with high substrate concentrations, converting 58% or more of the added carbon as acetate and ethanol to butyrate, butanol, and hexanoate. Semi-batch enrichment yielded hexanoate and octanoate as the most elongated products and microbial communities predominated by C. kluyveri and other Firmicutes genera not known to undergo chain elongation. Collectively, these results strongly suggest a niche for chain elongation in anaerobic soils that should not be overlooked in soil microbial ecology studies.
Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika
Authors: Tran Patricia Q , Bachand Samantha C , McIntyre Peter B , Kraemer Benjamin M , Vadeboncoeur Yvonne , Kimirei Ismael A , Tamatamah Rashid , McMahon Katherine D , Anantharaman Karthik 
Published: February 2021

Abstract
Lake Tanganyika (LT) is the largest tropical freshwater lake, and the largest body of anoxic freshwater on Earth’s surface. LT’s mixed oxygenated surface waters float atop a permanently anoxic layer and host rich animal biodiversity. However, little is known about microorganisms inhabiting LT’s 1470 meter deep water column and their contributions to nutrient cycling, which affect ecosystem-level function and productivity. Here, we applied genome-resolved metagenomics and environmental analyses to link specific taxa to key biogeochemical processes across a vertical depth gradient in LT. We reconstructed 523 unique metagenome-assembled genomes (MAGs) from 34 bacterial and archaeal phyla, including many rarely observed in freshwater lakes. We identified sharp contrasts in community composition and metabolic potential with an abundance of typical freshwater taxa in oxygenated mixed upper layers, and Archaea and uncultured Candidate Phyla in deep anoxic waters. Genomic capacity for nitrogen and sulfur cycling was abundant in MAGs recovered from anoxic waters, highlighting microbial contributions to the productive surface layers via recycling of upwelled nutrients, and greenhouse gases such as nitrous oxide. Overall, our study provides a blueprint for incorporation of aquatic microbial genomics in the representation of tropical freshwater lakes, especially in the context of ongoing climate change, which is predicted to bring increased stratification and anoxia to freshwater lakes.
Knockout of ASPP2 promotes DEN-induced hepatocarcinogenesis via the NF-κB pathway in mice
Authors: Wang Shanshan , Kou Buxin , Chai Mengyin , Gao Yuxue , Lin Xuejun , Yin Ling , Chen Dexi , Liu Xiaoni 
Published: February 2021

AbstractApoptosis-stimulating protein p53 2 (ASPP2) is a member of the p53-binding protein family, which is closely related to tumor development. However, the precise mechanism of ASPP2 in liver inflammation and tumorigenesis remains largely unclear. We aimed to characterize the mechanistic significance and clinical implication of ASPP2 in hepatitis and hepatocellular carcinoma (HCC). In this study, ASPP2 knockout (APKO) mice were generated to confirm the role of ASPP2 in the development of hepatitis and HCC. Liver tissues from mice were analyzed by immunohistochemistry, Western blotting, proteomic analysis, ChIP-Seq, and qRT-PCR to evaluate the role of ASPP2 in DEN-induced hepatitis and HCC. We found that APKO promoted the formation of hepatitis/hepatocarcinoma and the increased expression of proinflammatory factors. The proteomics and Western blotting results showed that APKO activated the NF-κB signaling pathway. Further, ChIP-Seq results revealed that NF-κB target genes were dramatically increased in APKO mice. In contrast, blockade of the NF-κB pathway by QNZ reduced the expression of proinflammatory factors and the susceptibility of APKO mice to DEN-induced hepatocarcinogenesis. These results suggested that the absence of ASPP2 activates the NF-κB pathway to promote the occurrence of DEN-induced hepatocarcinogenesis, indicating that ASPP2 may be a potential target for the treatment of hepatocarcinoma.
Cyclic quantum causal models
Authors: Barrett Jonathan , Lorenz Robin , Oreshkov Ognyan 
Published: February 2021

AbstractCausal reasoning is essential to science, yet quantum theory challenges it. Quantum correlations violating Bell inequalities defy satisfactory causal explanations within the framework of classical causal models. What is more, a theory encompassing quantum systems and gravity is expected to allow causally nonseparable processes featuring operations in indefinite causal order, defying that events be causally ordered at all. The first challenge has been addressed through the recent development of intrinsically quantum causal models, allowing causal explanations of quantum processes – provided they admit a definite causal order, i.e. have an acyclic causal structure. This work addresses causally nonseparable processes and offers a causal perspective on them through extending quantum causal models to cyclic causal structures. Among other applications of the approach, it is shown that all unitarily extendible bipartite processes are causally separable and that for unitary processes, causal nonseparability and cyclicity of their causal structure are equivalent.
Forecasting influenza activity using machine-learned mobility map
Authors: Venkatramanan Srinivasan , Sadilek Adam , Fadikar Arindam , Barrett Christopher L. , Biggerstaff Matthew , Chen Jiangzhuo , Dotiwalla Xerxes , Eastham Paul , Gipson Bryant , Higdon Dave , Kucuktunc Onur , Lieber Allison , Lewis Bryan L. , Reynolds Zane , Vullikanti Anil K. , Wang Lijing , Marathe Madhav 
Published: February 2021

AbstractHuman mobility is a primary driver of infectious disease spread. However, existing data is limited in availability, coverage, granularity, and timeliness. Data-driven forecasts of disease dynamics are crucial for decision-making by health officials and private citizens alike. In this work, we focus on a machine-learned anonymized mobility map (hereon referred to as AMM) aggregated over hundreds of millions of smartphones and evaluate its utility in forecasting epidemics. We factor AMM into a metapopulation model to retrospectively forecast influenza in the USA and Australia. We show that the AMM model performs on-par with those based on commuter surveys, which are sparsely available and expensive. We also compare it with gravity and radiation based models of mobility, and find that the radiation model’s performance is quite similar to AMM and commuter flows. Additionally, we demonstrate our model’s ability to predict disease spread even across state boundaries. Our work contributes towards developing timely infectious disease forecasting at a global scale using human mobility datasets expanding their applications in the area of infectious disease epidemiology.
Manganese co-limitation of phytoplankton growth and major nutrient drawdown in the Southern Ocean
Authors: Browning Thomas J. , Achterberg Eric P. , Engel Anja , Mawji Edward 
Published: February 2021

AbstractResidual macronutrients in the surface Southern Ocean result from restricted biological utilization, caused by low wintertime irradiance, cold temperatures, and insufficient micronutrients. Variability in utilization alters oceanic CO2 sequestration at glacial-interglacial timescales. The role for insufficient iron has been examined in detail, but manganese also has an essential function in photosynthesis and dissolved concentrations in the Southern Ocean can be strongly depleted. However, clear evidence for or against manganese limitation in this system is lacking. Here we present results from ten experiments distributed across Drake Passage. We found manganese (co-)limited phytoplankton growth and macronutrient consumption in central Drake Passage, whilst iron limitation was widespread nearer the South American and Antarctic continental shelves. Spatial patterns were reconciled with the different rates and timescales for removal of each element from seawater. Our results suggest an important role for manganese in modelling Southern Ocean productivity and understanding major nutrient drawdown in glacial periods.
Live-cell single particle tracking of PRC1 reveals a highly dynamic system with low target site occupancy
Authors: Huseyin Miles K. , Klose Robert J. 
Published: February 2021

AbstractPolycomb repressive complex 1 (PRC1) is an essential chromatin-based repressor of gene transcription. How PRC1 engages with chromatin to identify its target genes and achieve gene repression remains poorly defined, representing a major hurdle to our understanding of Polycomb system function. Here, we use genome engineering and single particle tracking to dissect how PRC1 binds to chromatin in live mouse embryonic stem cells. We observe that PRC1 is highly dynamic, with only a small fraction stably interacting with chromatin. By integrating subunit-specific dynamics, chromatin binding, and abundance measurements, we discover that PRC1 exhibits low occupancy at target sites. Furthermore, we employ perturbation approaches to uncover how specific components of PRC1 define its kinetics and chromatin binding. Together, these discoveries provide a quantitative understanding of chromatin binding by PRC1 in live cells, suggesting that chromatin modification, as opposed to PRC1 complex occupancy, is central to gene repression.
Construction of intracellular asymmetry and asymmetric division in Escherichia coli
Authors: Lin Da-Wei , Liu Yang , Lee Yue-Qi , Yang Po-Jiun , Ho Chia-Tse , Hong Jui-Chung , Hsiao Jye-Chian , Liao Der-Chien , Liang An-Jou , Hung Tzu-Chiao , Chen Yu-Chuan , Tu Hsiung-Lin , Hsu Chao-Ping , Huang Hsiao-Chun 
Published: February 2021

AbstractThe design principle of establishing an intracellular protein gradient for asymmetric cell division is a long-standing fundamental question. While the major molecular players and their interactions have been elucidated via genetic approaches, the diversity and redundancy of natural systems complicate the extraction of critical underlying features. Here, we take a synthetic cell biology approach to construct intracellular asymmetry and asymmetric division in Escherichia coli, in which division is normally symmetric. We demonstrate that the oligomeric PopZ from Caulobacter crescentus can serve as a robust polarized scaffold to functionalize RNA polymerase. Furthermore, by using another oligomeric pole-targeting DivIVA from Bacillus subtilis, the newly synthesized protein can be constrained to further establish intracellular asymmetry, leading to asymmetric division and differentiation. Our findings suggest that the coupled oligomerization and restriction in diffusion may be a strategy for generating a spatial gradient for asymmetric cell division.
High-speed three-dimensional photoacoustic computed tomography for preclinical research and clinical translation
Authors: Lin Li , Hu Peng , Tong Xin , Na Shuai , Cao Rui , Yuan Xiaoyun , Garrett David C. , Shi Junhui , Maslov Konstantin , Wang Lihong V. 
Published: February 2021

AbstractPhotoacoustic computed tomography (PACT) has generated increasing interest for uses in preclinical research and clinical translation. However, the imaging depth, speed, and quality of existing PACT systems have previously limited the potential applications of this technology. To overcome these issues, we developed a three-dimensional photoacoustic computed tomography (3D-PACT) system that features large imaging depth, scalable field of view with isotropic spatial resolution, high imaging speed, and superior image quality. 3D-PACT allows for multipurpose imaging to reveal detailed angiographic information in biological tissues ranging from the rodent brain to the human breast. In the rat brain, we visualize whole brain vasculatures and hemodynamics. In the human breast, an in vivo imaging depth of 4 cm is achieved by scanning the breast within a single breath hold of 10 s. Here, we introduce the 3D-PACT system to provide a unique tool for preclinical research and an appealing prototype for clinical translation.
TDCS effects on pointing task learning in young and old adults
Authors: Kaminski E. , Engelhardt M. , Hoff M. , Steele C. , A.Villringer  , Ragert P. 
Published: February 2021

AbstractSkill increase in motor performance can be defined as explicitly measuring task success but also via more implicit measures of movement kinematics. Even though these measures are often related, there is evidence that they represent distinct concepts of learning. In the present study, the effect of multiple tDCS-sessions on both explicit and implicit measures of learning are investigated in a pointing task in 30 young adults (YA) between 27.07 ± 3.8 years and 30 old adults (OA) between 67.97 years ± 5.3 years. We hypothesized, that OA would show slower explicit skill learning indicated by higher movement times/lower accuracy and slower implicit learning indicated by higher spatial variability but profit more from anodal tDCS compared with YA. We found age-related differences in movement time but not in accuracy or spatial variability. TDCS did not facilitate learning neither in explicit nor implicit parameters. However, contrary to our hypotheses, we found tDCS-associated higher accuracy only in YA but not in spatial variability. Taken together, our data shows limited overlapping of tDCS effects in explicit and implicit skill parameters. Furthermore, it supports the assumption that tDCS is capable of producing a performance-enhancing brain state at least for explicit skill acquisition.
High-temperature high-pressure microfluidic system for rapid screening of supercritical CO2 foaming agents
Authors: Gizzatov Ayrat , Pierobon Scott , AlYousef Zuhair , Jian Guoqing , Fan Xingyu , Abedini Ali , Abdel-Fattah Amr I. 
Published: February 2021

AbstractCO2 foam helps to increase the viscosity of CO2 flood fluid and thus improve the process efficiency of the anthropogenic greenhouse gas’s subsurface utilization and sequestration. Successful CO2 foam formation mandates the development of high-performance chemicals at close to reservoir conditions, which in turn requires extensive laboratory tests and evaluations. This work demonstrates the utilization of a microfluidic reservoir analogue for rapid evaluation and screening of commercial surfactants (i.e., Cocamidopropyl Hydroxysultaine, Lauramidopropyl Betaine, Tallow Amine Ethoxylate, N,N,N′ Trimethyl-N′-Tallow-1,3-diaminopropane, and Sodium Alpha Olefin Sulfonate) based on their performance to produce supercritical CO2 foam at high salinity, temperature, and pressure conditions. The microfluidic analogue was designed to represent the pore sizes of the geologic reservoir rock and to operate at 100 °C and 13.8 MPa. Values of the pressure drop across the microfluidic analogue during flow of the CO2 foam through its pore network was used to evaluate the strength of the generated foam and utilized only milliliters of liquid. The transparent microfluidic pore network allows in-situ quantitative visualization of CO2 foam to calculate its half-life under static conditions while observing if there is any damage to the pore network due to precipitation and blockage. The microfluidic mobility reduction results agree with those of foam loop rheometer measurements, however, the microfluidic approach provided more accurate foam stability data to differentiate the foaming agent as compared with conventional balk testing. The results obtained here supports the utility of microfluidic systems for rapid screening of chemicals for carbon sequestration or enhanced oil recovery operations.
Hemostatic and antibacterial PVA/Kaolin composite sponges loaded with penicillin–streptomycin for wound dressing applications
Authors: Tamer Tamer M. , Sabet Maysa M. , Omer Ahmed M. , Abbas Eman , Eid Alaa I. , Mohy-Eldin Mohamed S. , Hassan Mohamed A. 
Published: February 2021

AbstractHemorrhage is the major hindrance over the wound healing, which triggers microbial infections and might provoke traumatic death. Herein, new hemostatic and antibacterial PVA/Kaolin composite sponges were crosslinked using a freeze-thawing approach and boosted by penicillin–streptomycin (Pen-Strep). Physicochemical characteristics of developed membranes were analyzed adopting Fourier transformed infrared spectroscopy (FT-IR), scanning electron microscopy (SEM), a thermal gravimetric analyzer (TGA), and differential scanning calorimetry (DSC). Furthermore, the impacts of kaolin concentrations on porosity, swelling behavior, gel fraction, and degradation of the membranes were investigated. SEM analyses revealed a spongy-like structure of hydrogels associated with high dispersion of kaolin inside PVA matrix. The thermal characteristics of PVA/Kaolin were significantly ameliorated compared to the prime PVA. Moreover, the results exhibited significant variations of swelling performance, surface roughness and pore capacity due to the alterations of kaolin contents. Besides, the adhesive strength ability was manifestly enhanced for PVA-K0.1 sponge. Biomedical evaluations including antibacterial activity, blood clotting index and thrombogenicity of the membranes were studied. The contact of PVA/Kaolin to blood revealed notable augmentation in blood clotting. Furthermore, the incorporation of kaolin into PVA presented mild diminution in antibacterial activities. Moreover, PVA/Kaolin composites illustrated no cellular toxicity towards fibroblast cells. These remarkable features substantiate that the PVA-K0.1 sponge could be applied as a multifunctional wound dressing.
Asymptotic freedom and noninteger dimensionality
Authors: Kak Subhash 
Published: February 2021

AbstractThis paper shows that below a critical value of dimensionality that lies between two and three, the potential between objects begins to fall as the energy levels increase. For dimensionality below two, the potential becomes constant irrespective of separation and the force between them disappears, which represents a new paradigm of asymptotic freedom. Since asymptotic freedom is at the basis of many applications such as those associated with strange metals, unconventional superconductors, and fractional quantum Hall states, the new paradigm can have novel applications. It also is of relevance to the study of anomalous mechanical effects that are important in metamaterials.
Role of landslides on the volume balance of the Nepal 2015 earthquake sequence
Authors: Valagussa A. , Frattini P. , Valbuzzi E. , Crosta G. B. 
Published: February 2021

AbstractThe 7.8 Mw earthquake that struck Nepal on April 25th, 2015 triggered over 21,000 landslides over an area of more than 25,000 km2. These landslides contributed to mass wasting, partially compensating the tectonic uplift by the earthquake. In this paper we quantify the volume balance resulting from the 2015 earthquake uplift (or subsidence) and landslide erosion. Starting from a new complete earthquake-induced landslide inventory, we calculated landslide volume by adopting different strategies for low-mobility and high-mobility landslides, considering also the potential supply of sediments to the drainage network. The results show that the contribution of earthquake-induced landslides to erosion is about one order of magnitude smaller than the vertical coseismic displacement. We found landslide volume values, due to the 2015 Nepal earthquake, ranging between 251 (− 15/ + 16) Mm3 up to 1503 (− 183/ + 210) Mm3 based on the adopted method, and a volume due to coseismic vertical displacement of 2134 (± 1269) Mm3 for the whole area. The volume balance of the 2015 Nepal earthquake is strongly dominated by tectonic displacement. We show that these estimates depend on several uncertainties. We identified and quantified uncertainties related to: (1) the choice of empirical volume-area scaling relationships and their parameters; (2) the completeness and quality of landslide inventory through comparison with available inventories; (3) the approach adopted for the assessment of elongated landslide volume; (4) the InSAR displacement data.
Removal of diclofenac from aqueous solutions by adsorption on thermo-plasma expanded graphite
Authors: Cuccarese Marco , Brutti Sergio , De Bonis Angela , Teghil Roberto , Mancini Ignazio Marcello , Masi Salvatore , Caniani Donatella 
Published: February 2021

AbstractThe adsorption of diclofenac on thermo-plasma expanded graphite (a commercial product) from water solutions was investigated. The adsorbent material was characterized by SEM, TEM, BET, Raman and X-ray diffraction analyses. Typical diffractogram and Raman spectrum of graphitic material, dimension of 24.02 nm as crystallite dimension and a surface area of 47 m2 g−1were obtained. The effect of pH on the adsorption capacity was evaluated in the range 1–7 and the adsorption mechanism was described by kinetic and isothermal studies. Pseudo-second order and Dubinin–Radushkevich models agreed with theoretical values of adsorption capacity (i.e. 400 and 433 mg g−1, respectively) and resulted to be the best fit for kinetics and isothermal experimental data. The thermodynamics of the process was evaluated by plotting the adsorption capacity/concentration ratio at the equilibrium as a function of different values of the multiplicative inverse of temperature. Moreover, the adsorbent regeneration was also investigated, comparing two different remediation techniques. Solvent washing performed with NaOH 0.2 M and thermo-treatment carried out by heating in an oven at 105 °C for 2 h and then at 200 °C for 4 h. The thermo-treatment was the best technique to regenerate the adsorbent, ensuring same performance after 4 cycles of use and regeneration.
One-pot self-assembly synthesis of Ni-doped ordered mesoporous carbon for quantitative hydrogenation of furfural to furfuryl alcohol
Authors: Tang Yiwei , Qiu Mo , Yang Jirui , Shen Feng , Wang Xiaoqi , Qi Xinhua 
Published: February 2021

Ni-Doped OMC with high catalytic activity and stability for furfural hydrogenation to furfuryl alcohol was prepared by a one-pot evaporation-induced self-assembly process with biomass-derived gallic acid as carbon precursor and Ni2+ as crosslinker.