bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Modified Time Domain Random Walk Approach for Simulating Colloid Behavior in Fractures: Method Development and Verification
Authors: Yosri Ahmed , Dickson‐Anderson Sarah , El‐Dakhakhni Wael 
Published: June 2020

AbstractColloids are ubiquitous in groundwater systems, and understanding their behavior is of critical importance as they can pose a threat to human and environmental health. Extensive research has been conducted to model colloid behavior in fractures leading to the development of a number of analytical solutions, albeit for single fractures. However, the application of these analytical solutions at the network scale has not yet been established; thus, fracture networks are modeled using numerical techniques that are verified in single fractures first. Time domain random walk (TDRW) is a Lagrangian‐based approach originally designed to simulate solute transport in single fractures considering advection, dispersion, and matrix diffusion. The present study develops a modified TDRW approach (MTDRW) to consider colloid‐specific transport mechanisms based on an analytical solution describing colloid behavior in single fractures. The MTDRW approach was validated through simulating the behavior of (i) monodisperse colloids in a synthetic, single fracture with and without matrix diffusion; (ii) polydisperse colloids in a synthetic, single fracture with impermeable matrix; and (iii) monodisperse colloids in a synthetic impermeable fracture network. In all three cases, the MTDRW approach replicated the results of analytical solutions in single fractures and the semianalytical solution in fracture networks. The MTDRW approach is expected to enhance the reliability of colloid transport modeling due to its capacity to simulate the physiochemical heterogeneity across the network. This is required to (i) evaluate the aquifer vulnerability to colloid migration; (ii) predict the aquifer resilience under contamination events; and (iii) develop effective planning, management, and remediation strategies.
Ibuprofen mediates histone modification to diminish cancer cell stemness properties via a COX2-dependent manner
Authors: Shen Wenzhi , Zhang Xiaoyuan , Du Renle , Gao Wenjuan , Wang Juan , Bao Yonghua , Yang Wancai , Luo Na , Li Jianjun 
Published: June 2020

Abstract
Background
The anticancer potential of ibuprofen has created a broad interest to explore the clinical benefits of ibuprofen in cancer therapy. However, the current understanding of the molecular mechanisms involved in the anticancer potential of ibuprofen remains limited.

Methods
Cancer stemness assays to validate ibuprofen function in vitro and in vivo. Histone modification assays to check the effect of ibuprofen on histone acetylation/methylation, as well as the activity of HDAC and KDM6A/B. Inhibitors’ in vivo assays to evaluate therapeutic effects of various inhibitors’ combination manners.

Results
In our in vitro studies, we report that ibuprofen diminishes cancer cell stemness properties that include reducing the ALDH + subpopulation, side population and sphere formation in three cancer types. In our in vivo studies, we report that ibuprofen decreases tumour growth, metastasis and prolongs survival. In addition, our results showed that ibuprofen inhibits inflammation-related stemness gene expression (especially ICAM3) identified by a high-throughput siRNA platform. In regard to the underlying molecular mechanism of action, we report that ibuprofen reduces HDACs and histone demethylase (KDM6A/B) expression that mediates histone acetylation and methylation, and suppresses gene expression via a COX2-dependent way. In regard to therapeutic strategies, we report that ibuprofen combined HDAC/HDM inhibitors prevents cancer progression in vivo.

Conclusions
The aforementioned findings suggest a molecular model that explains how ibuprofen diminishes cancer cell stemness properties. These may provide novel targets for therapeutic strategies involving ibuprofen in the prevention of cancer progression.
BIK drives an aggressive breast cancer phenotype through sublethal apoptosis and predicts poor prognosis of ER-positive breast cancer
Authors: Pandya Vrajesh , Githaka John Maringa , Patel Namrata , Veldhoen Richard , Hugh Judith , Damaraju Sambasivarao , McMullen Todd , Mackey John , Goping Ing Swie 
Published: June 2020

AbstractApoptosis is fundamental to normal animal development and is the target for many anticancer therapies. Recent studies have explored the consequences of “failed apoptosis” where the apoptotic program is initiated but does not go to completion and does not cause cell death. Nevertheless, this failed apoptosis induces DNA double-strand breaks generating mutations that facilitate tumorigenesis. Whether failed apoptosis is relevant to clinical disease is unknown. BCL-2 interacting killer (BIK) is a stress-induced BH3-only protein that stimulates apoptosis in response to hormone and growth factor deprivation, hypoxia, and genomic stress. It was unclear whether BIK promotes or suppresses tumor survival within the context of breast cancer. We investigated this and show that BIK induces failed apoptosis with limited caspase activation and genomic damage in the absence of extensive cell death. Surviving cells acquire aggressive phenotypes characterized by enrichment of cancer stem-like cells, increased motility and increased clonogenic survival. Furthermore, by examining six independent cohorts of patients (total n = 969), we discovered that high BIK mRNA and protein levels predicted clinical relapse of Estrogen receptor (ER)-positive cancers, which account for almost 70% of all breast cancers diagnosed but had no predictive value for hormone receptor-negative (triple-negative) patients. Thus, this study identifies BIK as a biomarker for tumor recurrence of ER-positive patients and provides a potential mechanism whereby failed apoptosis contributes to cancer aggression.
Zoledronic acid regulates the synthesis and secretion of IL-1β through Histone methylation in macrophages
Authors: Yang Xiaojie , Xu Xing , Chen Jun , Wang Qing , Wang Guangfei , Ai Xuemin , Wang Xu , Pan Jinsong 
Published: June 2020

AbstractLong-term administration of nitrogen-containing bisphosphonates increases the risk of detrimental side effects, such as bisphosphonate-related osteonecrosis of the jaw (BRONJ). BRONJ development is associated with inflammation, but its pathophysiology remains unknown. Here, we examined whether histone methylation is responsible for zoledronic acid (Zol)-induced inflammatory responses. We found that Kdm6a and Kdm6b markedly increased interleukin 1β expression and Gasdermin D cleavage, which are both activated by Caspase 1, in macrophages. Inhibitors of Kdm6a and Kdm6b robustly abolished Zol-enhanced interleukin 1β synthesis and secretion from macrophages. When Kdm6a and Kdm6b were pharmacologically inhibited in vivo, poor healing of the alveolar socket and inflammatory responses were ameliorated in Zol-treated mice. Taken together, we showed the pathologic role of Kdm6a and Kdm6b in Zol-promoted inflammatory responses and demonstrated that Kdm6a and Kdm6b are potential therapeutic targets for the treatment of BRONJ.
Interfacial atomic layers for full emergence of interfacial Dzyaloshinskii–Moriya interaction
Authors: Park Yong-Keun , Kim Joo-Sung , Nam Yune-Seok , Jeon Seyyoung , Park Jung-Hyun , Kim Kyoung-Whan , Lee Hyun-Woo , Min Byoung-Chul , Choe Sug-Bong 
Published: June 2020

AbstractInterfacial phenomena play decisive roles in modern science and technology as the scale of the material shrinks down to a few atomic layers. Such minute nanostructures require a more comprehensive understanding beyond the conventional concepts of interfaces and interfacial phenomena generated at interfaces. From a series of a few-atomic-layer-thick magnetic films, we experimentally demonstrate that, contrary to the common notion, interfacial phenomena require a finite thickness for their full emergence. The layer-thickness dependences reveal that the interfacial Dzyaloshinskii–Moriya interaction (DMI) begins to appear with increasing thickness, and emerges completely at a thickness of 2–3 atomic layers, at which the magnitude is maximized. This result implies that the DMI is suppressed when the “bulk” layer adjacent to the interface is thinner than the threshold thickness. The existence of the threshold thickness indicates the need to refine conventional perspectives on interfacial phenomena, and imposes the lowest structural bound and optimum thickness to maximize interfacial effects for technological applications.
Real-time tracking reveals catalytic roles for the two DNA binding sites of Rad51
Authors: Ito Kentaro , Murayama Yasuto , Kurokawa Yumiko , Kanamaru Shuji , Kokabu Yuichi , Maki Takahisa , Mikawa Tsutomu , Argunhan Bilge , Tsubouchi Hideo , Ikeguchi Mitsunori , Takahashi Masayuki , Iwasaki Hiroshi 
Published: June 2020

AbstractDuring homologous recombination, Rad51 forms a nucleoprotein filament on single-stranded DNA to promote DNA strand exchange. This filament binds to double-stranded DNA (dsDNA), searches for homology, and promotes transfer of the complementary strand, producing a new heteroduplex. Strand exchange proceeds via two distinct three-strand intermediates, C1 and C2. C1 contains the intact donor dsDNA whereas C2 contains newly formed heteroduplex DNA. Here, we show that the conserved DNA binding motifs, loop 1 (L1) and loop 2 (L2) in site I of Rad51, play distinct roles in this process. L1 is involved in formation of the C1 complex whereas L2 mediates the C1–C2 transition, producing the heteroduplex. Another DNA binding motif, site II, serves as the DNA entry position for initial Rad51 filament formation, as well as for donor dsDNA incorporation. Our study provides a comprehensive molecular model for the catalytic process of strand exchange mediated by eukaryotic RecA-family recombinases.
Identification of interferon-stimulated genes that attenuate Ebola virus infection
Authors: Kuroda Makoto , Halfmann Peter J. , Hill-Batorski Lindsay , Ozawa Makoto , Lopes Tiago J. S. , Neumann Gabriele , Schoggins John W. , Rice Charles M. , Kawaoka Yoshihiro 
Published: June 2020

AbstractThe West Africa Ebola outbreak was the largest outbreak ever recorded, with over 28,000 reported infections; this devastating epidemic emphasized the need to understand the mechanisms to counteract virus infection. Here, we screen a library of nearly 400 interferon-stimulated genes (ISGs) against a biologically contained Ebola virus and identify several ISGs not previously known to affect Ebola virus infection. Overexpression of the top ten ISGs attenuates virus titers by up to 1000-fold. Mechanistic studies demonstrate that three ISGs interfere with virus entry, six affect viral transcription/replication, and two inhibit virion formation and budding. A comprehensive study of one ISG (CCDC92) that shows anti-Ebola activity in our screen reveals that CCDC92 can inhibit viral transcription and the formation of complete virions via an interaction with the viral protein NP. Our findings provide insights into Ebola virus infection that could be exploited for the development of therapeutics against this virus.
Transfer functions linking neural calcium to single voxel functional ultrasound signal
Authors: Aydin Ali-Kemal , Haselden William D. , Goulam Houssen Yannick , Pouzat Christophe , Rungta Ravi L. , Demené Charlie , Tanter Mickael , Drew Patrick J. , Charpak Serge , Boido Davide 
Published: June 2020

AbstractFunctional ultrasound imaging (fUS) is an emerging technique that detects changes of cerebral blood volume triggered by brain activation. Here, we investigate the extent to which fUS faithfully reports local neuronal activation by combining fUS and two-photon microscopy (2PM) in a co-registered single voxel brain volume. Using a machine-learning approach, we compute and validate transfer functions between dendritic calcium signals of specific neurons and vascular signals measured at both microscopic (2PM) and mesoscopic (fUS) levels. We find that transfer functions are robust across a wide range of stimulation paradigms and animals, and reveal a second vascular component of neurovascular coupling upon very strong stimulation. We propose that transfer functions can be considered as reliable quantitative reporters to follow neurovascular coupling dynamics.
The global lake area, climate, and population dataset
Authors: Meyer Michael F. , Labou Stephanie G. , Cramer Alli N. , Brousil Matthew R. , Luff Bradley T. 
Published: June 2020

AbstractAn increasing population in conjunction with a changing climate necessitates a detailed understanding of water abundance at multiple spatial and temporal scales. Remote sensing has provided massive data volumes to track fluctuations in water quantity, yet contextualizing water abundance with other local, regional, and global trends remains challenging by often requiring large computational resources to combine multiple data sources into analytically-friendly formats. To bridge this gap and facilitate future freshwater research opportunities, we harmonized existing global datasets to create the Global Lake area, Climate, and Population (GLCP) dataset. The GLCP is a compilation of lake surface area for 1.42 + million lakes and reservoirs of at least 10 ha in size from 1995 to 2015 with co-located basin-level temperature, precipitation, and population data. The GLCP was created with FAIR (findable, accessible, interoperable, reusable) data principles in mind and retains unique identifiers from parent datasets to expedite interoperability. The GLCP offers critical data for basic and applied investigations of lake surface area and water quantity at local, regional, and global scales.
Characteristic patterns of EEG oscillations in sheep (Ovis aries) induced by ketamine may explain the psychotropic effects seen in humans
Authors: Nicol A. U. , Morton A. J. 
Published: June 2020

AbstractKetamine is a valuable anaesthetic and analgesic that in recent years has gained notoriety as a recreational drug. Recently, ketamine has also been proposed as a novel treatment for depression and post-traumatic stress disorder. Beyond its anaesthetic actions, however, the effects of ketamine on brain activity have rarely been probed. Here we examined the cortical electroencephalography (EEG) response to ketamine of 12 sheep. Following ketamine administration, EEG changes were immediate and widespread, affecting the full extent of the EEG frequency spectrum measured (0–125 Hz). After recovery from sedation during which low frequency activity dominated, the EEG was characterised by short periods (2–3 s) of alternating low (<14 Hz) and high (>35 Hz) frequency oscillation. This alternating EEG rhythm phase is likely to underlie the dissociative actions of ketamine, since it is during this phase that ketamine users report hallucinations. At the highest intravenous dose used (24 mg/kg), in 5/6 sheep we observed a novel effect of ketamine, namely the complete cessation of cortical EEG activity. This persisted for up to several minutes, after which cortical activity resumed. This phenomenon is likely to explain the ‘k-hole’, a state of oblivion likened to a near death experience that is keenly sought by ketamine abusers.
Comparison of lung microbiota between antineutrophil cytoplasmic antibody-associated vasculitis and sarcoidosis
Authors: Fukui Shoichi , Morimoto Shimpei , Ichinose Kunihiro , Nakashima Shota , Ishimoto Hiroshi , Hara Atsuko , Kakugawa Tomoyuki , Sakamoto Noriho , Tsuji Yoshika , Aramaki Toshiyuki , Koga Tomohiro , Kawashiri Shin-ya , Iwamoto Naoki , Tamai Mami , Nakamura Hideki , Origuchi Tomoki , Ueki Yukitaka , Suzuki Shino , Mukae Hiroshi , Kawakami Atsushi 
Published: June 2020

AbstractMicrobial involvement in the pathogenesis have been suggested in both antineutrophil cytoplasmic antibody-associated vasculitis (AAV) and sarcoidosis, both of which have lung involvement. However, exhaustive research to assess the bacteria in the lung in AAV and in sarcoidosis have not been performed. We sought to elucidate the distinct dysbiotic lung microbiota between AAV and sarcoidosis. We used 16S rRNA gene high-throughput sequencing to obtain the bacterial community composition of bronchoalveolar lavage fluid (BALF) in patients with AAV (n = 16) compared to patients with sarcoidosis (n = 21). The patients had not undergone therapy with immunosuppressive medication when their BALF was acquired. No difference was observed in α-diversity between patients with AAV and patients with sarcoidosis when using all the detected taxa. We defined the taxa of the oral cavity by using the data of oral microbiota of healthy individuals from the Human Microbiome Project (HMP). The analysis using only oral taxa made the difference in α-diversity between AAV and sarcoidosis clearer compared with those using all the detected taxa. Besides, the analysis using detected taxa except for oral taxa also made the difference in α-diversity between AAV and sarcoidosis clearer compared with those using all the detected taxa. A linear negative relationship between the α-diversity and Birmingham vasculitis activity score (BVAS) was detected in the AAV group. The observed p-value for the effect of the disease groups on the ß-diversity was small while the effect of other factors including sex and smoking status did not have small p-values. By excluding oral taxa from all the detected taxa, we found a cluster mainly consisted of sarcoidosis patients which was characterized with microbial community monopolized by Erythrobacteraceae family. Our results suggested the importance of considering the influence of oral microbiota in evaluating lung microbiota.
The potential of FBC fly ashes to reduce CO2 emissions
Authors: Uliasz-Bocheńczyk Alicja , Mokrzycki Eugeniusz 
Published: June 2020

AbstractThe production of electricity and heat in Poland is the reason why the commercial power industry is the largest emitter of CO2. At the same time, significant amounts of solid by-products of combustion, which can be used to bind CO2 by mineral carbonation, are generated during the production processes. The article presents the results of research on mineral sequestration of CO2 (suspension-CO2) using fluidized bed combustion (FBC) fly ashes from hard coal combustion. The analyzed fluidized bed combustion (FBC) fly ashes were characterized by a significant free CaO content (1.7–6.8%) and a high CO2 binding potential ranging from 9.7 to 15.7%. In the case of fluidized bed combustion (FBC) fly ashes suspensions, the basic product of the carbonation process is calcium carbonate, which is clearly indicated by the results of the phase composition determination of solidified suspensions of fluidized bed combustion (FBC) fly ashes. The degree of carbonation, i.e. the degree of CO2 binding, calculated on the basis of the calcium carbonate content, in the analyzed suspensions was up to 1.1%. Mineral carbonation also reduces the leachability of pollutants such as: Zn, Cu, Pb, Ni, As, Hg, Cd, Cr, Cl, and SO42-. The pH is also reduced from about 12 to about 9. Aqueous suspensions of fluidized bed combustion (FBC) fly ashes with introduced CO2 can potentially be used in underground mining. These activities are in line with the concepts of Carbon Capture and Utilization and the idea of circular economy.
Geochemical evidence for a widespread mantle re-enrichment 3.2 billion years ago: implications for global-scale plate tectonics
Authors: Gamal El Dien Hamed , Doucet Luc S. , Murphy J. Brendan , Li Zheng-Xiang 
Published: June 2020

AbstractProgressive mantle melting during the Earth’s earliest evolution led to the formation of a depleted mantle and a continental crust enriched in highly incompatible elements. Re-enrichment of Earth’s mantle can occur when continental crustal materials begin to founder into the mantle by either subduction or, to a lesser degree, by delamination processes, profoundly affecting the mantle’s trace element and volatile compositions. Deciphering when mantle re-enrichment/refertilization became a global-scale process would reveal the onset of efficient mass transfer of crust to the mantle and potentially when plate tectonic processes became operative on a global-scale. Here we document the onset of mantle re-enrichment/refertilization by comparing the abundances of petrogenetically significant isotopic values and key ratios of highly incompatible elements compared to lithophile elements in Archean to Early-Proterozoic mantle-derived melts (i.e., basalts and komatiites). Basalts and komatiites both record a rapid-change in mantle chemistry around 3.2 billion years ago (Ga) signifying a fundamental change in Earth geodynamics. This rapid-change is recorded in Nd isotopes and in key trace element ratios that reflect a fundamental shift in the balance between fluid-mobile and incompatible elements (i.e., Ba/La, Ba/Nb, U/Nb, Pb/Nd and Pb/Ce) in basaltic and komatiitic rocks. These geochemical proxies display a significant increase in magnitude and variability after ~3.2 Ga. We hypothesize that rapid increases in mantle heterogeneity indicate the recycling of supracrustal materials back into Earth’s mantle via subduction. Our new observations thus point to a ≥ 3.2 Ga onset of global subduction processes via plate tectonics.
Persistence of plastic debris and its colonization by bacterial communities after two decades on the abyssal seafloor
Authors: Krause S. , Molari M. , Gorb E. V. , Gorb S. N. , Kossel E. , Haeckel M. 
Published: June 2020

AbstractThe fate of plastic debris entering the oceans is largely unconstrained. Currently, intensified research is devoted to the abiotic and microbial degradation of plastic floating near the ocean surface for an extended period of time. In contrast, the impacts of environmental conditions in the deep sea on polymer properties and rigidity are virtually unknown. Here, we present unique results of plastic items identified to have been introduced into deep-sea sediments at a water depth of 4150 m in the eastern equatorial Pacific Ocean more than two decades ago. The results, including optical, spectroscopic, physical and microbial analyses, clearly demonstrate that the bulk polymer materials show no apparent sign of physical or chemical degradation. Solely the polymer surface layers showed reduced hydrophobicity, presumably caused by microbial colonization. The bacterial community present on the plastic items differed significantly (p < 0.1%) from those of the adjacent natural environment by a dominant presence of groups requiring steep redox gradients (Mesorhizobium, Sulfurimonas) and a remarkable decrease in diversity. The establishment of chemical gradients across the polymer surfaces presumably caused these conditions. Our findings suggest that plastic is stable over extended times under deep-sea conditions and that prolonged deposition of polymer items at the seafloor may induce local oxygen depletion at the sediment-water interface.