bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of tropical forest disturbance on the competitive interactions within a diverse ant community
Authors: Gray Ross E. J. , Ewers Robert M. , Boyle Michael J. W. , Chung Arthur Y. C. , Gill Richard J. 
Published: March 2018

AbstractUnderstanding how anthropogenic disturbance influences patterns of community composition and the reinforcing interactive processes that structure communities is important to mitigate threats to biodiversity. Competition is considered a primary reinforcing process, yet little is known concerning disturbance effects on competitive interaction networks. We examined how differences in ant community composition between undisturbed and disturbed Bornean rainforest, is potentially reflected by changes in competitive interactions over a food resource. Comparing 10 primary forest sites to 10 in selectively-logged forest, we found higher genus richness and diversity in the primary forest, with 18.5% and 13.0% of genera endemic to primary and logged respectively. From 180 hours of filming bait cards, we assessed ant-ant interactions, finding that despite considered aggression over food sources, the majority of ant interactions were neutral. Proportion of competitive interactions at bait cards did not differ between forest type, however, the rate and per capita number of competitive interactions was significantly lower in logged forest. Furthermore, the majority of genera showed large changes in aggression-score with often inverse relationships to their occupancy rank. This provides evidence of a shuffled competitive network, and these unexpected changes in aggressive relationships could be considered a type of competitive network re-wiring after disturbance.
Artifact Rejection Methodology Enables Continuous, Noninvasive Measurement of Gastric Myoelectric Activity in Ambulatory Subjects
Authors: Gharibans Armen A. , Smarr Benjamin L. , Kunkel David C. , Kriegsfeld Lance J. , Mousa Hayat M. , Coleman Todd P. 
Published: March 2018

AbstractThe increasing prevalence of functional and motility gastrointestinal (GI) disorders is at odds with bottlenecks in their diagnosis, treatment, and follow-up. Lack of noninvasive approaches means that only specialized centers can perform objective assessment procedures. Abnormal GI muscular activity, which is coordinated by electrical slow-waves, may play a key role in symptoms. As such, the electrogastrogram (EGG), a noninvasive means to continuously monitor gastric electrical activity, can be used to inform diagnoses over broader populations. However, it is seldom used due to technical issues: inconsistent results from single-channel measurements and signal artifacts that make interpretation difficult and limit prolonged monitoring. Here, we overcome these limitations with a wearable multi-channel system and artifact removal signal processing methods. Our approach yields an increase of 0.56 in the mean correlation coefficient between EGG and the clinical “gold standard”, gastric manometry, across 11 subjects (p < 0.001). We also demonstrate this system’s usage for ambulatory monitoring, which reveals myoelectric dynamics in response to meals akin to gastric emptying patterns and circadian-related oscillations. Our approach is noninvasive, easy to administer, and has promise to widen the scope of populations with GI disorders for which clinicians can screen patients, diagnose disorders, and refine treatments objectively.
Millet manuring as a driving force for the Late Neolithic agricultural expansion of north China
Authors: Wang Xin , Fuller Benjamin T. , Zhang Pengcheng , Hu Songmei , Hu Yaowu , Shang Xue 
Published: March 2018

AbstractResearch in to the nature of Neolithic agriculture in China is often focused on topics such as the domestication and spread of cereal crops and the reconstruction of human and animal diets in the past. Field management practices, such as organic manuring, have not been systematically investigated in Chinese archaeology. Here we present an isotopic dataset for archaeological foxtail millet (Setaria italica) and common millet (Panicum miliaceum) grains as well as associated faunal remains (both domesticated and wild) from seven sites in the Baishui Valley of north China, in order to find direct evidence of organic manuring during the Late Neolithic period. The elevated nitrogen isotope values of the millet grains (5500-3500 cal BP) in comparison with the estimated local vegetation indicates that millets were organically manured by animal dung, mostly likely originating from domestic pigs. Considering the low nitrogen contents of loess soils and their unsuitability for intensive cultivation, this organic manuring by animal dung would have played a key role in maintaining soil productivity and crop yield, which was necessary to support the demands of agriculture and cultural expansion during the Late Neolithic on the Loess Plateau of China.
Genetic homogeneity of the invasive lionfish across the Northwestern Atlantic and the Gulf of Mexico based on Single Nucleotide Polymorphisms
Authors: Pérez-Portela R. , Bumford A. , Coffman B. , Wedelich S. , Davenport M. , Fogg A. , Swenarton M. K. , Coleman F. , Johnston M. A. , Crawford D. L. , Oleksiak M. F. 
Published: March 2018

AbstractDespite the devastating impact of the lionfish (Pterois volitans) invasion on NW Atlantic ecosystems, little genetic information about the invasion process is available. We applied Genotyping by Sequencing techniques to identify 1,220 single nucleotide polymorphic sites (SNPs) from 162 lionfish samples collected between 2013 and 2015 from two areas chronologically identified as the first and last invaded areas in US waters: the east coast of Florida and the Gulf of Mexico. We used population genomic analyses, including phylogenetic reconstruction, Bayesian clustering, genetic distances, Discriminant Analyses of Principal Components, and coalescence simulations for detection of outlier SNPs, to understand genetic trends relevant to the lionfish’s long-term persistence. We found no significant differences in genetic structure or diversity between the two areas (FSTp-values > 0.01, and t-test p-values > 0.05). In fact, our genomic analyses showed genetic homogeneity, with enough gene flow between the east coast of Florida and Gulf of Mexico to erase previous signals of genetic divergence detected between these areas, secondary spreading, and bottlenecks in the Gulf of Mexico. These findings suggest rapid genetic changes over space and time during the invasion, resulting in one panmictic population with no signs of divergence between areas due to local adaptation.
Galantamine anti-colitic effect: Role of alpha-7 nicotinic acetylcholine receptor in modulating Jak/STAT3, NF-κB/HMGB1/RAGE and p-AKT/Bcl-2 pathways
Authors: Wazea Shakeeb A. , Wadie Walaa , Bahgat Ashraf K. , El-Abhar Hanan S. 
Published: March 2018

AbstractVagal stimulation controls systemic inflammation and modulates the immune response in different inflammatory conditions, including inflammatory bowel diseases (IBD). The released acetylcholine binds to alpha-7 nicotinic acetylcholine receptor (α7 nAChR) to suppress pro-inflammatory cytokines. This provides a new range of potential therapeutic approaches for controlling inflammatory responses. The present study aimed to assess whether galantamine (Galan) anti-inflammatory action involves α7 nAChR in a 2,4,6-trinitrobenzene sulfonic acid (TNBS) model of colitis and to estimate its possible molecular pathways. Rats were assigned into normal, TNBS, sulfasalazine (Sulfz), Galan treated (10 mg/kg), methyllycaconitine (MLA; 5.6 mg/kg), and MLA + Galan groups. Drugs were administered orally once per day (11 days) and colitis was induced on the 8thday. Galan reduced the TNBS-induced ulceration, colon mass index, colonic MDA, neutrophils adhesion and infiltration (ICAM-1/MPO), inflammatory mediators (NF-κB, TNF-α, HMGB1, and RAGE), while increased the anti-apoptotic pathway (p-Akt/Bcl-2). Mechanistic study revealed that Galan increased the anti-inflammatory cytokine IL-10, phosphorylated Jak2, while reduced the inflammation controller SOCS3. However, combining MLA with Galan abrogated the beneficial anti-inflammatory/anti-apoptotic signals. The results of the present study indicate that Galan anti-inflammatory/-apoptotic/ -oxidant effects originate from the stimulation of the peripheral α7 nAChR, with the involvement of the Jak2/SOCS3 signaling pathway.
Abrupt Climate Change in an Oscillating World
Authors: Bathiany S. , Scheffer M. , van Nes E. H. , Williamson M. S. , Lenton T. M. 
Published: March 2018

AbstractThe notion that small changes can have large consequences in the climate or ecosystems has become popular as the concept of tipping points. Typically, tipping points are thought to arise from a loss of stability of an equilibrium when external conditions are slowly varied. However, this appealingly simple view puts us on the wrong foot for understanding a range of abrupt transitions in the climate or ecosystems because complex environmental systems are never in equilibrium. In particular, they are forced by diurnal variations, the seasons, Milankovitch cycles and internal climate oscillations. Here we show how abrupt and sometimes even irreversible change may be evoked by even small shifts in the amplitude or time scale of such environmental oscillations. By using model simulations and reconciling evidence from previous studies we illustrate how these phenomena can be relevant for ecosystems and elements of the climate system including terrestrial ecosystems, Arctic sea ice and monsoons. Although the systems we address are very different and span a broad range of time scales, the phenomena can be understood in a common framework that can help clarify and unify the interpretation of abrupt shifts in the Earth system.
Comparison of the Biological Characteristics of Mesenchymal Stem Cells Derived from the Human Placenta and Umbilical Cord
Authors: Wu Mingjun , Zhang Ruifan , Zou Qing , Chen Yaoyao , Zhou Min , Li Xingjie , Ran Ran , Chen Qiang 
Published: March 2018

AbstractMesenchymal stem/stromal cells (MSCs) derived from placental tissue show great therapeutic potential and have been used in medical treatment, but the similarity and differences between the MSCs derived from various parts of the placenta remain unclear. In this study, we compared MSCs derived from different perinatal tissues, including the umbilical cord (UC), amniotic membrane (AM), chorionic plate (CP) and decidua parietalis (DP). Using human leukocyte antigen (HLA) typing and karyotype analysis, we found that the first three cell types were derived from the foetus, while the MSCs from the decidua parietalis were derived from the maternal portion of the placental tissue. Our results indicate that both foetal and maternal MSCs share a similar phenotype and multi-lineage differentiation potential, but foetal MSCs show a significantly higher expansion capacity than do maternal MSCs. Furthermore, MSCs from all sources showed significant differences in the levels of several paracrine factors.
Lactobacillus paracasei CNCM I-3689 reduces vancomycin-resistant Enterococcus persistence and promotes Bacteroidetes resilience in the gut following antibiotic challenge
Authors: Crouzet Laureen , Derrien Muriel , Cherbuy Claire , Plancade Sandra , Foulon Mélanie , Chalin Benjamin , van Hylckama Vlieg Johan E. T. , Grompone Gianfranco , Rigottier-Gois Lionel , Serror Pascale 
Published: March 2018

AbstractEnterococci, in particular vancomycin-resistant enterococci (VRE), are a leading cause of hospital-acquired infections. Promoting intestinal resistance against enterococci could reduce the risk of VRE infections. We investigated the effects of two Lactobacillus strains to prevent intestinal VRE. We used an intestinal colonisation mouse model based on an antibiotic-induced microbiota dysbiosis to mimic enterococci overgrowth and VRE persistence. Each Lactobacillus spp. was administered daily to mice starting one week before antibiotic treatment until two weeks after antibiotic and VRE inoculation. Of the two strains, Lactobacillus paracasei CNCM I-3689 decreased significantly VRE numbers in the feces demonstrating an improvement of the reduction of VRE. Longitudinal microbiota analysis showed that supplementation with L. paracasei CNCM I-3689 was associated with a better recovery of members of the phylum Bacteroidetes. Bile salt analysis and expression analysis of selected host genes revealed increased level of lithocholate and of ileal expression of camp (human LL-37) upon L. paracasei CNCM I-3689 supplementation. Although a direct effect of L. paracasei CNCM I-3689 on the VRE reduction was not ruled out, our data provide clues to possible anti-VRE mechanisms supporting an indirect anti-VRE effect through the gut microbiota. This work sustains non-antibiotic strategies against opportunistic enterococci after antibiotic-induced dysbiosis.
Landau-Zener-Stückelberg interference in coherent charge oscillations of a one-electron double quantum dot
Authors: Ota Takeshi , Hitachi Kenichi , Muraki Koji 
Published: March 2018

AbstractLandau-Zener (LZ) transition has received renewed interest as an alternative approach to control single-qubit states. An LZ transition occurs when a system passes through an avoided crossing that arises from quantum mechanical coupling of two levels, taking the system to a coherent superposition of the two states. Then, multiple LZ transitions induce interference known as Landau-Zener-Stückelberg (LZS) interference whose amplitude strongly depends on the velocity or adiabaticity of the passage. Here, we study the roles of LZ transitions and LZS interference in coherent charge oscillations of a one-electron semiconductor double quantum dot by time-domain experiments using standard rectangular voltage pulses. By employing density matrix simulations, we show that, in the standard setup using rectangular pulses, even a small distortion of the pulse can give rise to LZ transitions and hence LZS interference, which significantly enhances the measured oscillation amplitude. We further show experimentally that the nature of the coherent charge oscillations changes from Rabi-type to LZS oscillations with increasing pulse distortion. Our results thus demonstrate that it is essential to take into account LZS interference for both precise control of charge qubits and correct interpretation of measurement results.
Adaptive nodes enrich nonlinear cooperative learning beyond traditional adaptation by links
Authors: Sardi Shira , Vardi Roni , Goldental Amir , Sheinin Anton , Uzan Herut , Kanter Ido 
Published: March 2018

AbstractPhysical models typically assume time-independent interactions, whereas neural networks and machine learning incorporate interactions that function as adjustable parameters. Here we demonstrate a new type of abundant cooperative nonlinear dynamics where learning is attributed solely to the nodes, instead of the network links which their number is significantly larger. The nodal, neuronal, fast adaptation follows its relative anisotropic (dendritic) input timings, as indicated experimentally, similarly to the slow learning mechanism currently attributed to the links, synapses. It represents a non-local learning rule, where effectively many incoming links to a node concurrently undergo the same adaptation. The network dynamics is now counterintuitively governed by the weak links, which previously were assumed to be insignificant. This cooperative nonlinear dynamic adaptation presents a self-controlled mechanism to prevent divergence or vanishing of the learning parameters, as opposed to learning by links, and also supports self-oscillations of the effective learning parameters. It hints on a hierarchical computational complexity of nodes, following their number of anisotropic inputs and opens new horizons for advanced deep learning algorithms and artificial intelligence based applications, as well as a new mechanism for enhanced and fast learning by neural networks.
Evaluating the efficacy of a landscape scale feral cat control program using camera traps and occupancy models
Authors: Comer Sarah , Speldewinde Peter , Tiller Cameron , Clausen Lucy , Pinder Jeff , Cowen Saul , Algar Dave 
Published: March 2018

AbstractThe impact of introduced predators is a major factor limiting survivorship and recruitment of many native Australian species. In particular, the feral cat and red fox have been implicated in range reductions and population declines of many conservation dependent species across Australia, including ground-nesting birds and small to medium-sized mammals. The impact of predation by feral cats since their introduction some 200 years ago has altered the structure of native fauna communities and led to the development of landscape-scale threat abatement via baiting programs with the feral cat bait, Eradicat. Demonstrating the effectiveness of broad-scale programs is essential for managers to fine tune delivery and timing of baiting. Efficacy of feral cat baiting at the Fortescue Marsh in the Pilbara, Western Australia was tested using camera traps and occupancy models. There was a significant decrease in probability of site occupancy in baited sites in each of the five years of this study, demonstrating both the effectiveness of aerial baiting for landscape-scale removal of feral cats, and the validity of camera trap monitoring techniques for detecting changes in feral cat occupancy during a five-year baiting program.
Predicting Urban Reservoir Levels Using Statistical Learning Techniques
Authors: Obringer Renee , Nateghi Roshanak 
Published: March 2018

AbstractUrban water supplies are critical to the growth of the city and the wellbeing of its citizens. However, these supplies can be vulnerable to hydrological extremes, such as droughts and floods, especially if they are the main source of water for the city. Maintaining these supplies and preparing for future conditions is a crucial task for water managers, but predicting hydrological extremes is a challenge. This study tested the abilities of eight statistical learning techniques to predict reservoir levels, given the current hydroclimatic conditions, and provide inferences on the key predictors of reservoir levels. The results showed that random forest, an ensemble, tree-based method, was the best algorithm for predicting reservoir levels. We initially developed the models using Lake Sidney Lanier (Atlanta, Georgia) as the test site; however, further analysis demonstrated that the model based on the random forest algorithm was transferable to other reservoirs, specifically Eagle Creek (Indianapolis, Indiana) and Lake Travis (Austin, Texas). Additionally, we found that although each reservoir was impacted differently, streamflow, city population, and El Niño/Southern Oscillation (ENSO) index were repeatedly among the most important predictors. These are critical variables which can be used by water managers to recognize the potential for reservoir level changes.
Direct antiviral properties of TLR ligands against HBV replication in immune-competent hepatocytes
Authors: Lucifora Julie , Bonnin Marc , Aillot Ludovic , Fusil Floriane , Maadadi Sarah , Dimier Laura , Michelet Maud , Floriot Océane , Ollivier Anaïs , Rivoire Michel , Ait-Goughoulte Malika , Daffis Stéphane , Fletcher Simon P. , Salvetti Anna , Cosset François-Loïc , Zoulim Fabien , Durantel David 
Published: March 2018

AbstractCurrent therapies for chronic hepatitis B virus (HBV) infections are effective at decreasing the viral load in serum, but do not lead to viral eradication. Recent studies highlighted the therapeutic or “adjuvant” potential of immune-modulators. Our aim was to explore the direct anti-HBV effect of Toll-Like-Receptors (TLR) agonists in hepatocytes. HBV-infected primary human hepatocytes (PHH) or differentiated HepaRG cells (dHepaRG) were treated with various TLR agonists. Amongst all TLR ligands tested, Pam3CSK4 (TLR1/2-ligand) and poly(I:C)-(HMW) (TLR3/MDA5-ligand) were the best at reducing all HBV parameters. No or little viral rebound was observed after treatment arrest, implying a long-lasting effect on cccDNA. We also tested Riboxxol that features improved TLR3 specificity compared to poly(I:C)-(HMW). This agonist demonstrated a potent antiviral effect in HBV-infected PHH. Whereas, poly(I:C)-(HMW) and Pam3CSK4 mainly induced the expression of classical genes from the interferon or NF-κB pathway respectively, Riboxxol had a mixed phenotype. Moreover, TLR2 and TLR3 ligands can activate hepatocytes and immune cells, as demonstrated by antiviral cytokines produced by stimulated hepatocytes and peripheral blood mononuclear cells. In conclusion, our data highlight the potential of innate immunity activation in the direct control of HBV replication in hepatocytes, and support the development of TLR-based antiviral strategies.
Analysis of protein structure changes and quality regulation of surimi during gelation based on infrared spectroscopy and microscopic imaging
Authors: Wei Wei , Hu Wei , Zhang Xian-Yi , Zhang Feng-Ping , Sun Su-Qin , Liu Yuan , Xu Chang-Hua 
Published: March 2018

AbstractA developed Fourier transform infrared spectroscopy (FT-IR) was employed to investigate changes of protein conformation, which played significant roles in maintaining stable protein networks of white croaker surimi gel, exploring the relationship between protein conformation and surimi gel networks. Spectra of surimi and gels with different grades (A, AA, FA and SA) were analyzed by tri-step FT-IR method and peak-fitting of deconvolved and baseline corrected amide I bands (1600~1700 cm−1). The result showed that α-helix was the main conformation of surimi proteins. During surimi gelation, α-helix of myosin partially transformed into β-sheet, β-turn and random coil structures. β-sheet and random coil structures were the main protein conformations maintaining the structure of surimi gel, of which β-sheet made the main contribution to gel strength. Scanning electron microscopy (SEM) result revealed that surimi gels had a fibrous and homogeneous network structure. Moreover, ordered interconnections between three-dimensional proteins networks of gels were inclined to emerge in higher grade surimi, in agreement with the gel strength results. It was demonstrated that the tri-step FT-IR spectroscopy combined with peak-fitting could be applicable for exploration of surimi protein conformation changes during gelation to deepen understanding of its effect on gel quality.
Identification of The Aberrantly Expressed LncRNAs in Hepatocellular Carcinoma: A Bioinformatics Analysis Based on RNA-sequencing
Authors: Liao Hao-Tian , Huang Ji-Wei , Lan Tian , Wang Jin-Ju , Zhu Bo , Yuan Ke-Fei , Zeng Yong 
Published: March 2018

AbstractHepatocellular carcinoma (HCC) is one of the most prevalent subtypes of liver cancer worldwide. LncRNAs have been demonstrated to be associated with the progression of HCC, but a systematic identification and characterization of their clinical roles and molecular mechanisms in HCC has not been conducted. In this study, the aberrantly expressed lncRNAs in HCC tissues were analyzed based on TCGA RNA-seq data. 1162 lncRNAs were found to be aberrantly expressed in HCC tissues, including 232 down-regulated lncRNAs and 930 up-regulated lncRNAs. The top 5 lncRNAs with the highest diagnostic accuracy were further analyzed to evaluate their clinical value and potential mechanism in HCC. Kaplan-Meier curves showed that higher expressions of DDX11-AS1 and AC092171.4 were in correlation with poorer survival in HCC patients. Significant difference was also observed when comparing the expression levels of DDX11-AS1 and SFTA1P in different clinical parameters (p < 0.05). GO analysis showed that genes regulated by the 5 lncRNAs were enriched in certain pathways, such as PI3K pathway. Moreover, GSEA analysis on the expression of DDX11-AS1 showed that DDX11-AS1 affected the gene expressions involved in HCC proliferation, differentiation and cell cycle, indicating an essential role of DDX11-AS1 in hepatocarcinogenesis.