bluuebunny/crossref_metadata_2025_split huggingface dataset:
A review of the impact of exercise on treatment-related fatigue among patients receiving adjuvant radiotherapy for breast cancer
Authors: McNally Fiona , Shepherd Paul H. , Flood Terri 
Published: January 2019

AbstractPurposeTo evaluate the use of exercise in managing fatigue in breast cancer patients undergoing adjuvant radiotherapy. To explore the effectiveness of different exercise practices and explore how optimum management of fatigue might be achieved.MethodA CINAHL (Cumulative Index to Nursing and Allied Health Literature) database search of literature was undertaken and publications screened for retrieval with 24 qualifying for inclusion in the review.ResultsThere is evidence to support various forms of exercise including aerobic, resistance, alternative and combination exercise in the management of fatigue in early stage breast cancer patients undergoing adjuvant radiotherapy. The benefits of exercise for patients with later stage and metastatic disease is less clear and there is a lack of published research related to this category of patient.ConclusionExercise is considered a safe, non-pharmacological intervention for early stage breast cancer patients receiving adjuvant radiotherapy. Further investigation is required into optimum exercise interventions and the effectiveness and viability of supervised and unsupervised models. Patient centred tailored advice and guidance needs to be developed and effectively promoted by therapeutic radiographers in order for patients to fully realise the benefit.
Probabilistic DL Reasoning with Pinpointing Formulas: A Prolog-based Approach
Authors: ZESE RICCARDO , COTA GIUSEPPE , LAMMA EVELINA , BELLODI ELENA , RIGUZZI FABRIZIO 
Published: January 2019

AbstractWhen modeling real-world domains, we have to deal with information that is incomplete or that comes from sources with different trust levels. This motivates the need for managing uncertainty in the Semantic Web. To this purpose, we introduced a probabilistic semantics, named DISPONTE, in order to combine description logics (DLs) with probability theory. The probability of a query can be then computed from the set of its explanations by building a Binary Decision Diagram (BDD). The set of explanations can be found using thetableau algorithm, which has to handle non-determinism. Prolog, with its efficient handling of non-determinism, is suitable for implementing the tableau algorithm. TRILL and TRILLPare systems offering a Prolog implementation of the tableau algorithm. TRILLPbuilds apinpointing formulathat compactly represents the set of explanations and can be directly translated into a BDD. Both reasoners were shown to outperform state-of-the-art DL reasoners. In this paper, we present an improvement of TRILLP, named TORNADO, in which the BDD is directly built during the construction of the tableau, further speeding up the overall inference process. An experimental comparison shows the effectiveness of TORNADO. All systems can be tried online in the TRILL on SWISH web application athttp://trill.ml.unife.it/.
Effect of rice straw and/or nitrogen fertiliser inputs on methanogenic archaeal and denitrifying communities in a typical rice paddy soil
Authors: BAO Qiongli , DING Long-Jun , HUANG Yizong , XIAO Keqing 
Published: January 2019

ABSTRACTTo understand better the microbial functional populations which are involved in methanogenesis and denitrification in paddy soils with rice straw (RS) and/or nitrogen fertiliser (potassium nitrate, N) application, the dynamics of methanogens and the denitrifying community were monitored simultaneously during the incubation period. The results show that the community structure of methanogens remained relatively stable among treatments based on 16S rDNA analysis, but fluctuated based on 16S rRNA. The Methanocellaceae and Methanosarcinaceae dominated all treatments at 16S rDNA and 16S rRNA level, respectively. RS+N increased the relative abundance of Methanosaetaceae at the 16S rRNA level, while there was an increasing trend in that Methanomicrobiaceae following RS addition at the 16S rDNA level. RS and/or N did not significantly change the diversity of methanogens targeting both 16S rDNA and 16S rRNA. RS and RS+N increased copy numbers of methanogens targeting both 16S rDNA and 16S rRNA analyses. The community structure and abundance ofnirSandnosZ-containing denitrifiers, and the diversity ofnirS-containing denitrifiers was significantly altered only by the N treatment. These results indicate that the community structure, diversity and abundance of methanogens respond differently to RS addition at the 16S rDNA and 16S rRNA levels.
Implications for the Melting Phase Relations in the MgO‐FeO System at Core‐Mantle Boundary Conditions
Authors: Deng Jie , Miyazaki Yoshinori , Lee Kanani K. M. 
Published: January 2019

AbstractAt nearly 2,900‐km depth, the core‐mantle boundary (CMB) represents the largest density increase within the Earth going from a rocky mantle into an iron‐alloy core. This compositional change sets up steep temperature gradients, which in turn influences mantle flow, structure, and seismic velocities. Here we resolve the thermodynamic parameters of (Mg,Fe)O and compute the melting phase relations of the MgO‐FeO binary system at CMB conditions. Based on this phase diagram, we revisit iron infiltration into solid ferropericlase along the CMB by morphological instability and find that the length scale of infiltration is comparable with the high electrical conductivity layer inferred from core nutations. We also compute the (Mg,Fe)O‐SiO2 pseudo‐binary system and find that the solidus melting temperatures near the CMB decrease with FeO and SiO2 content, becoming potentially important for ultralow velocity zones. Therefore, an ultralow velocity zone composed of solid‐state bridgmanite and ferropericlase may be relatively enriched in MgO and depleted in SiO2 and FeO along a hot CMB.
Rates of Dynamic Recrystallization in Geologic Materials
Authors: Cross A. J. , Skemer P. 
Published: January 2019

AbstractGrain size reduction via dynamic recrystallization (DRX) is intimately related to the softening of crystalline materials under an applied stress, and plays a role in numerous geodynamic processes that involve strain‐weakening feedbacks. Despite its importance, few studies have provided empirical constraints on the rates of DRX and grain size reduction. Here we examine DRX rates using the Johnson‐Mehl‐Avrami‐Kolmogorov theory for phase transformation kinetics. Our analysis uses a compilation of published and newly‐derived DRX data from experimental studies on a wide range of geologic and engineering materials. We find that DRX rates are strongly dependent on the homologous temperature at which deformation occurs, with DRX occurring over a broad range of shear strains (0.01 < γ < 200), and more rapidly with increasing homologous temperature. Moreover, the experimental data can be described by a single fit to a modified form of the Avrami equation that incorporates homologous temperature dependence, implying that, to first order, DRX rates are largely material independent. We also examine the influence of stress, deformation work rate, crystal orientation, and initial grain size on DRX rates and compare DRX data from experimental and natural conditions. Overall, we show that microstructures can evolve over long transient intervals, and provide a framework for determining DRX kinetics from empirical data, which can ultimately be incorporated into geodynamic models of grain size evolution in the Earth.
Predictability of Ocean Heat Content From Electrical Conductance
Authors: Trossman D. S. , Tyler R. H. 
Published: January 2019

AbstractOcean heat content (OHC) is a key climate variable that needs to be monitored to know how Earth's energy imbalance is changing, yet observing OHC remains a challenge. The present study examines whether a depth integral of the ocean's electrical conductivity (“conductance”), which may be inferred from both in situ methods and satellite magnetometers over the global ocean, could help monitor OHC. The ocean's electrical conductivity locally depends on temperature, salinity, and pressure, but it is not as well known how the conductance depends on OHC and ocean salt content. By examining the output of an ocean state estimate shown to agree well with observations that have not been assimilated, this study evaluates the fundamental limitations of using perfectly known ocean conductance to predict OHC, rather than the challenges associated with accounting for observational error. It is found that the ocean's conductance and OHC fields are nonlinearly related but nevertheless highly correlated. A statistical framework tends to predict OHC more accurately than ocean salt content from ocean conductance in regions where conductivity is more sensitive to salinity than temperature. The annually (bidecadally) averaged OHC can be predicted from a combination of conductance and depth‐averaged conductivity ocean fields to within nearly 0.1% (1%) error globally and even more accurately in many poorly observed (e.g., ice‐covered) regions. Practical application of this statistical framework to monitor OHC requires examination of the effect of uncertainties in the observed bathymetry and ocean conductance, which vary with application.
Transactivation of human endogenous retroviruses by tumor viruses and their functions in virus-associated malignancies
Authors: Chen Jungang , Foroozesh Maryam , Qin Zhiqiang 
Published: January 2019

AbstractHuman endogenous retroviruses (HERVs), viral-associated sequences, are normal components of the human genome and account for 8–9% of our genome. These original provirus sequences can be transactivated to produce functional products. Several reactivated HERVs have been implicated in cancers and autoimmune diseases. An emerging body of literature supports a potential role of reactivated HERVs in viral diseases, in particular viral-associated neoplasms. Demystifying studies on the mechanism(s) of HERV reactivation could provide a new framework for the development of treatment and prevention strategies targeting virus-associated tumors. Although available data suggest that co-infection by other viruses, such as Kaposi’s Sarcoma-associated herpesvirus (KSHV) and Epstein–Barr virus (EBV), may be a crucial driving force to transactivate HERV boom, the mechanisms of action of viral infection-induced HERV transactivation and the contributions of HERVs to viral oncogenesis warrant further studies. Here, we review viral co-infection contributes to HERVs transactivation with focus on human viral infection associated oncogenesis and diseases, including the abilities of viral regulators involved in HERV reactivation, and physiological effects of viral infection response on HERV reactivation.
Mixotrophic protists display contrasted biogeographies in the global ocean
Authors: Faure Emile , Not Fabrice , Benoiston Anne-Sophie , Labadie Karine , Bittner Lucie , Ayata Sakina-Dorothée 
Published: January 2019

Abstract
Mixotrophy, or the ability to acquire carbon from both auto- and heterotrophy, is a widespread ecological trait in marine protists. Using a metabarcoding dataset of marine plankton from the global ocean, 318,054 mixotrophic metabarcodes represented by 89,951,866 sequences and belonging to 133 taxonomic lineages were identified and classified into four mixotrophic functional types: constitutive mixotrophs (CM), generalist non-constitutive mixotrophs (GNCM), endo-symbiotic specialist non-constitutive mixotrophs (eSNCM), and plastidic specialist non-constitutive mixotrophs (pSNCM). Mixotrophy appeared ubiquitous, and the distributions of the four mixotypes were analyzed to identify the abiotic factors shaping their biogeographies. Kleptoplastidic mixotrophs (GNCM and pSNCM) were detected in new zones compared to previous morphological studies. Constitutive and non-constitutive mixotrophs had similar ranges of distributions. Most lineages were evenly found in the samples, yet some of them displayed strongly contrasted distributions, both across and within mixotypes. Particularly divergent biogeographies were found within endo-symbiotic mixotrophs, depending on the ability to form colonies or the mode of symbiosis. We showed how metabarcoding can be used in a complementary way with previous morphological observations to study the biogeography of mixotrophic protists and to identify key drivers of their biogeography.
China’s coal mine methane regulations have not curbed growing emissions
Authors: Miller Scot M. , Michalak Anna M. , Detmers Robert G. , Hasekamp Otto P. , Bruhwiler Lori M. P. , Schwietzke Stefan 
Published: January 2019

AbstractAnthropogenic methane emissions from China are likely greater than in any other country in the world. The largest fraction of China’s anthropogenic emissions is attributable to coal mining, but these emissions may be changing; China enacted a suite of regulations for coal mine methane (CMM) drainage and utilization that came into full effect in 2010. Here, we use methane observations from the GOSAT satellite to evaluate recent trends in total anthropogenic and natural emissions from Asia with a particular focus on China. We find that emissions from China rose by 1.1 ± 0.4 Tg CH4 yr−1 from 2010 to 2015, culminating in total anthropogenic and natural emissions of 61.5 ± 2.7 Tg CH4 in 2015. The observed trend is consistent with pre-2010 trends and is largely attributable to coal mining. These results indicate that China’s CMM regulations have had no discernible impact on the continued increase in Chinese methane emissions.
Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria
Authors: Mutalik Vivek K. , Novichkov Pavel S. , Price Morgan N. , Owens Trenton K. , Callaghan Mark , Carim Sean , Deutschbauer Adam M. , Arkin Adam P. 
Published: January 2019

AbstractA major challenge in genomics is the knowledge gap between sequence and its encoded function. Gain-of-function methods based on gene overexpression are attractive avenues for phenotype-based functional screens, but are not easily applied in high-throughput across many experimental conditions. Here, we present Dual Barcoded Shotgun Expression Library Sequencing (Dub-seq), a method that uses random DNA barcodes to greatly increase experimental throughput. As a demonstration of this approach, we construct a Dub-seq library with Escherichia coli genomic DNA, performed 155 genome-wide fitness assays in 52 experimental conditions, and identified overexpression phenotypes for 813 genes. We show that Dub-seq data is reproducible, accurately recapitulates known biology, and identifies hundreds of novel gain-of-function phenotypes for E. coli genes, a subset of which we verified with assays of individual strains. Dub-seq provides complementary information to loss-of-function approaches and will facilitate rapid and systematic functional characterization of microbial genomes.
Ocean temperature impact on ice shelf extent in the eastern Antarctic Peninsula
Authors: Etourneau Johan , Sgubin Giovanni , Crosta Xavier , Swingedouw Didier , Willmott Verónica , Barbara Loïc , Houssais Marie-Noëlle , Schouten Stefan , Damsté Jaap S. Sinninghe , Goosse Hugues , Escutia Carlota , Crespin Julien , Massé Guillaume , Kim Jung-Hyun 
Published: January 2019

AbstractThe recent thinning and retreat of Antarctic ice shelves has been attributed to both atmosphere and ocean warming. However, the lack of continuous, multi-year direct observations as well as limitations of climate and ice shelf models prevent a precise assessment on how the ocean forcing affects the fluctuations of a grounded and floating ice cap. Here we show that a +0.3–1.5 °C increase in subsurface ocean temperature (50–400 m) in the northeastern Antarctic Peninsula has driven to major collapse and recession of the regional ice shelf during both the instrumental period and the last 9000 years. Our projections following the representative concentration pathway 8.5 emission scenario from the Fifth Assessment Report of the Intergovernmental Panel on Climate Change reveal a +0.3 °C subsurface ocean temperature warming within the coming decades that will undoubtedly accelerate ice shelf melting, including the southernmost sector of the eastern Antarctic Peninsula.
Regulation of substrate utilization and adiposity by Agrp neurons
Authors: Cavalcanti-de-Albuquerque João Paulo , Bober Jeremy , Zimmer Marcelo R. , Dietrich Marcelo O. 
Published: January 2019

AbstractThe type of nutrient utilized by the organism at any given time—substrate utilization—is a critical component of energy metabolism. The neuronal mechanisms involved in the regulation of substrate utilization in mammals are largely unknown. Here, we found that activation of hypothalamic Agrp neurons rapidly altered whole-body substrate utilization, increasing carbohydrate utilization, while decreasing fat utilization. These metabolic changes occurred even in the absence of caloric ingestion and were coupled to increased lipogenesis. Accordingly, inhibition of fatty acid synthase—a key enzyme that mediates lipogenesis—blunted the effects of Agrp neuron activation on substrate utilization. In pair-fed conditions during positive energy balance, activation of Agrp neurons improved metabolic efficiency, and increased weight gain and adiposity. Conversely, ablation of Agrp neurons impaired fat mass accumulation. These results suggest Agrp neurons regulate substrate utilization, contributing to lipogenesis and fat mass accumulation during positive energy balance.
An evolutionarily-conserved Wnt3/β-catenin/Sp5 feedback loop restricts head organizer activity in Hydra
Authors: Vogg Matthias C. , Beccari Leonardo , Iglesias Ollé Laura , Rampon Christine , Vriz Sophie , Perruchoud Chrystelle , Wenger Yvan , Galliot Brigitte 
Published: January 2019

AbstractPolyps of the cnidarian Hydra maintain their adult anatomy through two developmental organizers, the head organizer located apically and the foot organizer basally. The head organizer is made of two antagonistic cross-reacting components, an activator, driving apical differentiation and an inhibitor, preventing ectopic head formation. Here we characterize the head inhibitor by comparing planarian genes down-regulated when β-catenin is silenced to Hydra genes displaying a graded apical-to-basal expression and an up-regulation during head regeneration. We identify Sp5 as a transcription factor that fulfills the head inhibitor properties: leading to a robust multiheaded phenotype when knocked-down in Hydra, acting as a transcriptional repressor of Wnt3 and positively regulated by Wnt/β-catenin signaling. Hydra and zebrafish Sp5 repress Wnt3 promoter activity while Hydra Sp5 also activates its own expression, likely via β-catenin/TCF interaction. This work identifies Sp5 as a potent feedback loop inhibitor of Wnt/β-catenin signaling, a function conserved across eumetazoan evolution.
Differential damage and repair of DNA-adducts induced by anti-cancer drug cisplatin across mouse organs
Authors: Yimit Askar , Adebali Ogun , Sancar Aziz , Jiang Yuchao 
Published: January 2019

AbstractThe platinum-based drug cisplatin is a widely used first-line therapy for several cancers. Cisplatin interacts with DNA mainly in the form of Pt-d(GpG) di-adduct, which stalls cell proliferation and activates DNA damage response. Although cisplatin shows a broad spectrum of anticancer activity, its utility is limited due to acquired drug resistance and toxicity to non-targeted tissues. Here, by integrating genome-wide high-throughput Damage-seq, XR-seq, and RNA-seq approaches, along with publicly available epigenomic data, we systematically study the genome-wide profiles of cisplatin damage formation and excision repair in mouse kidney, liver, lung and spleen. We find different DNA damage and repair spectra across mouse organs, which are associated with tissue-specific transcriptomic and epigenomic profiles. The framework and the multi-omics data we present here constitute an unbiased foundation for understanding the mechanisms of cellular response to cisplatin. Our approach should be applicable for studying drug resistance and for tailoring cancer chemotherapy regimens.
Enhancement of Fixed-bed Flow Reactions under Microwave Irradiation by Local Heating at the Vicinal Contact Points of Catalyst Particles
Authors: Haneishi Naoto , Tsubaki Shuntaro , Abe Eriko , Maitani Masato M. , Suzuki Ei-ichi , Fujii Satoshi , Fukushima Jun , Takizawa Hirotsugu , Wada Yuji 
Published: January 2019

AbstractThe formation of local high temperature regions, or so-called “hot spots”, in heterogeneous reaction systems has been suggested as a critical factor in the enhancement of chemical reactions using microwave heating. In this paper, we report the generation of local high temperature regions between catalyst particles under microwave heating. First, we demonstrated that reaction rate of the dehydrogenation of 2-propanol over a magnetite catalyst was enhanced 17- (250 °C) to 38- (200 °C) fold when heated with microwave irradiation rather than an electrical furnace. Subsequently, the existence of microwave-generated specific local heating was demonstrated using a coupled simulation of the electromagnetic fields and heat transfer as well as in situ emission spectroscopy. Specific high-temperature regions were generated at the vicinal contact points of the catalyst particles due to the concentrated microwave electric field. We also directly observed local high temperature regions at the contact points of the particles during microwave heating of a model silicon carbide spherical material using in situ emission spectroscopy. We conclude that the generation of local heating at the contact points between the catalyst particles is a key factor for enhancing fixed-bed flow reactions under microwave irradiation.
Genome-Wide Transcriptome Landscape of Embryonic Brain-Derived Neural Stem Cells Exposed to Alcohol with Strain-Specific Cross-Examination in BL6 and CD1 Mice
Authors: Xu Wayne , Liyanage Vichithra R. B. , MacAulay Aaron , Levy Romina D. , Curtis Kyle , Olson Carl O. , Zachariah Robby M. , Amiri Shayan , Buist Marjorie , Hicks Geoffrey G. , Davie James R. , Rastegar Mojgan 
Published: January 2019

AbstractWe have previously reported the deregulatory impact of ethanol on global DNA methylation of brain-derived neural stem cells (NSC). Here, we conducted a genome-wide RNA-seq analysis in differentiating NSC exposed to different modes of ethanol exposure. RNA-seq results showed distinct gene expression patterns and canonical pathways induced by ethanol exposure and withdrawal. Short-term ethanol exposure caused abnormal up-regulation of synaptic pathways, while continuous ethanol treatment profoundly affected brain cells’ morphology. Ethanol withdrawal restored the gene expression profile of differentiating NSC without rescuing impaired expression of epigenetics factors. Ingenuity Pathway Analysis (IPA) analysis predicated that ethanol may impact synaptic functions via GABA receptor signalling pathway and affects neural system and brain morphology. We identified Sptbn2, Dcc, and Scn3a as candidate genes which may link alcohol-induced neuronal morphology to brain structural abnormalities, predicted by IPA analysis. Cross-examination of Scn3a and As3mt in differentiated NSC from two different mouse strains (BL6 and CD1) showed a consistent pattern of induction and reduction, respectively. Collectively, our study identifies genetic networks, which may contribute to alcohol-mediated cellular and brain structural dysmorphology, contributing to our knowledge of alcohol-mediated damage to central nervous system, paving the path for better understanding of FASD pathobiology.