bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dispersive Regimes of the Dicke Model
Authors: Barberena Diego , Lamata Lucas , Solano Enrique 
Published: August 2017

AbstractWe study two dispersive regimes of the Dicke model in the dynamics of N two-level atoms interacting with a bosonic mode for long interaction times. Firstly, we analyze the model for the regime in which the qubit frequencies are equal and smaller than the mode frequency, and for values of the coupling strength similar or larger than the mode frequency, namely, the deep strong coupling regime. Secondly, we address an interaction that is dependent on the photon number, where the coupling strength is comparable to the geometric mean of the qubit and mode frequencies. We show that the associated dynamics is analytically tractable and provide useful frameworks with which to analyze the system behavior. In the deep strong coupling regime, we unveil the structure of unexpected resonances for specific values of the coupling, present for N ≥ 2, and in the photon-number-dependent regime we demonstrate that all the nontrivial dynamical behavior occurs in the atomic degrees of freedom for a given Fock state. We verify these assertions with numerical simulations of the qubit population and photon-statistic dynamics.
Enhanced silicon availability leads to increased methane production, nutrient and toxicant mobility in peatlands
Authors: Reithmaier Gloria-Maria Susanne , Knorr Klaus-Holger , Arnhold Sebastian , Planer-Friedrich Britta , Schaller Jörg 
Published: August 2017

AbstractPeatlands perform important ecosystem functions, such as carbon storage and nutrient retention, which are affected, among other factors, by vegetation and peat decomposition. The availability of silicon (Si) in peatlands differs strongly, ranging from <1 to >25 mg L−1. Since decomposition of organic material was recently shown to be accelerated by Si, the aim of this study was to examine how Si influences decomposition of carbon and nutrient and toxicant mobilization in peatlands. We selected a fen site in Northern Bavaria with naturally bioavailable Si pore water concentrations of 5 mg/L and conducted a Si addition experiment. At a fourfold higher Si availability, dissolved organic carbon, carbon dioxide, and methane concentrations increased significantly. Furthermore, dissolved nitrogen, phosphorus, iron, manganese, cobalt, zinc, and arsenic concentrations were significantly higher under high Si availability. This enhanced mobilization may result from Si competing for binding sites but also from stronger reducing conditions, caused by accelerated respiration. The stronger reducing conditions also increased reduction of arsenate to arsenite and thus the mobility of this toxicant. Hence, higher Si availability is suggested to decrease carbon storage and increase nutrient and toxicant mobility in peatland ecosystems.
Analysis of spatial genetic variation reveals genetic divergence among populations of Primula veris associated to contrasting habitats
Authors: Deschepper Pablo , Brys Rein , Fortuna Miguel A. , Jacquemyn Hans 
Published: August 2017

AbstractGenetic divergence by environment is a process whereby selection causes the formation of gene flow barriers between populations adapting to contrasting environments and is often considered to be the onset of speciation. Nevertheless, the extent to which genetic differentiation by environment on small spatial scales can be detected by means of neutral markers is still subject to debate. Previous research on the perennial herb Primula veris has shown that plants from grassland and forest habitats showed pronounced differences in phenology and flower morphology, suggesting limited gene flow between habitats. To test this hypothesis, we sampled 33 populations of P. veris consisting of forest and grassland patches and used clustering techniques and network analyses to identify sets of populations that are more connected to each other than to other sets of populations and estimated the timing of divergence. Our results showed that spatial genetic variation had a significantly modular structure and consisted of four well-defined modules that almost perfectly coincided with habitat features. Genetic divergence was estimated to have occurred about 114 generations ago, coinciding with historic major changes in the landscape. Overall, these results illustrate how populations adapting to different environments become structured genetically within landscapes on small spatial scales.
Molecular mechanisms of atlastin-mediated ER membrane fusion revealed by a FRET-based single-vesicle fusion assay
Authors: Kim Kyung Tae , Moon Yeojin , Jang Yunsu , Lee Kang Taek , Lee Changwook , Jun Youngsoo , Lee Sanghwa 
Published: August 2017

AbstractHomotypic fusion of endoplasmic reticulum membranes is driven by atlastin GTPases; however, the underlying mechanism remains largely unknown. Here, using a FRET-based single-vesicle fusion assay with liposomes bearing the yeast atlastin Sey1p, we investigated the molecular mechanisms of atlastin-mediated membrane tethering and fusion. Although Sey1p-bearing proteoliposomes frequently underwent membrane tethering in a GTP hydrolysis-dependent manner as reported in studies using bulk assays, only a small fraction of the tethered liposomes proceeded to fusion. Strikingly, the rest of the tethered liposomes failed to fuse or dissociate. This stable tethering, however, did not require continued GTP hydrolysis because GTP omission and magnesium chelation did not disrupt tethering. Interestingly, an increased Sey1p density on the membrane markedly accelerated tethering but barely affected the fusion rate of the tethered liposomes, indicating that Sey1p requires additional factors to support efficient fusion in vivo. Finally, the assay also revealed that Sey1p-mediated liposome fusion occurs through hemifusion, suggesting the mechanistic conservation between biological membrane fusion events despite the existence of diverse fusogens.
Unconventional MAPK-GSK-3β Pathway Behind Atypical Epithelial-Mesenchymal Transition In Hepatocellular Carcinoma
Authors: Parveen Sana , Vedagiri Dhiviya , Nair Hitha Gopalan , Parthasarathy Haripriya , Harshan Krishnan Harinivas 
Published: August 2017

AbstractWe recently reported an atypical epithelial mesenchymal transition (EMT) in human hepatoma cell culture Huh7.5, which was non-responsive to the canonical EMT-transcription factors. Here we characterize major pathways regulating this atypical EMT through whole genome transcriptome profiling and molecular analysis, and identify a unique regulation of EMT by GSK-3β. Our analysis reveals remarkable suppression of several key liver-specific markers in Huh7.5M cells indicating that EMT not only changes the epithelial properties, but alters the characteristics associated with hepatocytes as well. One key finding of this study is that GSK-3β, a known antagonist to β-Catenin signaling and a major pro-apoptotic regulator, is critical for the maintenance of EMT in Huh7.5M cells as its inhibition reversed EMT. Importantly, through these studies we identify that maintenance of EMT by GSK-3β in Huh7.5M is regulated by p38MAPK and ERK1/2 that has not been reported elsewhere and is distinct from another metastatic non-hepatic cell line MDA-MB-231. These data showcase the existence of non-canonical mechanisms behind EMT. The atypicalness of this system underlines the existence of tremendous diversity in cancer-EMT and warrants the necessity to take a measured approach while dealing with metastasis and cancer drug resistance.
Detecting hybridization between sister species of Terebratulina (Brachiopoda, Cancellothyridoidea) in the North Atlantic: morphology versus molecules
Authors: Lüter Carsten , Ebeling Nina A. , Aberhan Martin 
Published: August 2017

AbstractInvestigating samples of the cancellothyridid brachiopod Terebratulina collected during the IceAGE (Me85/3) expedition of RV METEOR at the continental shelf around Iceland with both morphometrical and molecular methods, we were for the first time able to detect a hybridization event between brachiopod sister species, which are thought to have separated 60 MYA. Terebratulina retusa and T. septentrionalis can clearly be distinguished on the basis of consistent species-specific molecular signatures in both mitochondrial and nuclear markers, whereas morphometrical analyses proved to be less reliable for species determination than previously thought. Two out of 28 specimens were identified as offspring of a one-way hybridization event between T. retusa eggs and T. septentrionalis sperm. Whereas the fossil record of Terebratulina in the North Atlantic region is too fragmentary to reconstruct the history of the hybridization event, the different life history traits of the two species and current oceanographic conditions around Iceland offer plausible explanations for the occurrence of crossbreeds in this common brachiopod genus.
The NADPH oxidase NOX2 mediates loss of parvalbumin interneurons in traumatic brain injury: human autoptic immunohistochemical evidence
Authors: Schiavone Stefania , Neri Margherita , Trabace Luigia , Turillazzi Emanuela 
Published: August 2017

AbstractPharmacological interventions for traumatic brain injury (TBI) are limited. Together with parvalbumin (PV) loss, increased production of reactive oxygen species (ROS) by the NADPH oxidase NOX enzymes represents a key step in TBI. Here, we investigated the contribution of NOX2-derived oxidative stress to the loss of PV immunoreactivity associated to TBI, performing immunohistochemistry for NOX2, 8-hydroxy-2′-deoxyguanosine (8OHdG) and PV on post mortem brain samples of subjects died following TBI, subjects died from spontaneous intracerebral hemorrhage (SICH) and controls (CTRL). We detected an increased NOX2 expression and 8OHdG immunoreactivity in subjects died from TBI with respect to CTRL and SICH. NOX2 increase was mainly observed in GABAergic PV-positive interneurons, with a minor presence in microglia. No significant differences in other NADPH oxidase isoforms (NOX1 and NOX4) were detected among experimental groups. NOX2-derived oxidative stress elevation appeared a specific TBI-induced phenomenon, as no alterations in the nitrosative pathway were detected. Our results suggest that NOX2-derived oxidative stress might play a crucial role in the TBI-induced loss of PV-positive interneurons.
Highly efficient up-conversion luminescence in Er3+/Yb3+ co-doped Na5Lu9F32 single crystals by vertical Bridgman method
Authors: He Shinan , Xia Haiping , Zhang Jianli , Zhu Yongsheng , Chen Baojiu 
Published: August 2017

AbstractEr3+/Yb3+ co-doped Na5Lu9F32 single crystals with different concentrations of Yb3+ ions were prepared to investigate their phase structure, up-conversion (UC) properties and mechanism of UC luminescence by Bridgman method. Under 980 nm near-infrared (NIR) excitation, three sharp UC emission bands topping at green ~525 nm, ~548 nm and red ~669 nm were obtained in Er3+/Yb3+ doped Na5Lu9F32 single crystals which are attributing to the transitions of 2H11/2 → 4I15/2, 4S3/2 → 4I15/2 and 4F9/2 → 4I15/2, respectively. The quadratic dependence of pump power on UC emission indicated that two-photon process is in charge of the transition from excited state of Yb3+ ions to lower state of Er3+ ion in Na5Lu9F32 single crystals. The long-accepted mechanism for the production of red and green emissions through up-conversion (UC) under 980 nm excitation in Er3+/Yb3+ co-doped materials apply in the Na5Lu9F32 host was displayed. The enhancement of the red emission was observed due to a cross-relaxation (CR) process of the form: 4F7/2 + 4I11/2 → 4F9/2 + 4F9/2. Furthermore, an ideal yellowish green light performance could be achieved with 1.0 mol% Er3+ doped certain Yb3+ concentrations samples, and its external quantum efficiency approached to 6.80% under 5.5 Wcm−2 980 nm excitation which can be applied in developing UC displays for electro-optical devices.
Global methylation correlates with clinical status in multiple sclerosis patients in the first year of IFNbeta treatment
Authors: Pinto-Medel María Jesús , Oliver-Martos Begoña , Urbaneja-Romero Patricia , Hurtado-Guerrero Isaac , Ortega-Pinazo Jesús , Serrano-Castro Pedro , Fernández Óscar , Leyva Laura 
Published: August 2017

AbstractThe alteration of DNA methylation patterns are a key component of disease onset and/or progression. Our objective was to evaluate the differences in Long Interspersed Nuclear Element-1 (LINE-1) methylation levels, as a surrogate marker of global DNA methylation, between multiple sclerosis (MS) patients and healthy controls. In addition, we assessed the association of LINE-1 methylation with clinical disease activity in patients treated with IFNbeta (IFNβ). We found that individuals with high levels of LINE-1 methylation showed 6-fold increased risk of suffering MS. Additionally, treated MS patients who bear high LINE-1 methylation levels had an 11-fold increased risk of clinical activity. Moreover, a negative correlation between treatment duration and percentage of LINE-1 methylation, that was statistically significant exclusively in the group of patients without clinical activity, was observed. Our data suggest that in MS patients, a slight global DNA hypermethylation occurs that may be related to the pathophysiology of the disease. In addition, global DNA methylation levels could play a role as a biomarker for the differential clinical response to IFNβ.
Ocular fundus pulsations within the posterior rat eye: Chorioscleral motion and response to elevated intraocular pressure
Authors: Augustin Marco , Fialová Stanislava , Fischak Corinna , Schmetterer Leopold , Hitzenberger Christoph K. , Baumann Bernhard 
Published: August 2017

AbstractA multi-functional optical coherence tomography (OCT) approach is presented to determine ocular fundus pulsations as an axial displacement between the retina and the chorioscleral complex in the albino rat eye. By combining optical coherence elastography and OCT angiography (OCTA), we measure subtle deformations in the nanometer range within the eye and simultaneously map retinal and choroidal perfusion. The conventional OCT reflectivity contrast serves as a backbone to segment the retina and to define several slabs which are subsequently used for quantitative ocular pulsation measurements as well as for a qualitative exploration of the multi-functional OCT image data. The proposed concept is applied in healthy albino rats as well as in rats under acute elevation of the intraocular pressure (IOP). The evaluation of this experiment revealed an increased pulsatility and deformation between the retinal and chorioscleral complex while increasing the IOP level from 15 mmHg to 65 mmHg. At IOP levels exceeding 65 mmHg, the pulsatility decreased significantly and retinal as well as choroidal perfusion vanished in OCTA. Furthermore, the evaluation of the multi-parametric experiment revealed a spatial correlation between fundus pulsatility and choroidal blood flow. This indicates that the assessed pulsatility may be a valuable parameter describing the choroidal perfusion.
Osteocyte regulation of orthodontic force-mediated tooth movement via RANKL expression
Authors: Shoji-Matsunaga Ayumi , Ono Takehito , Hayashi Mikihito , Takayanagi Hiroshi , Moriyama Keiji , Nakashima Tomoki 
Published: August 2017

AbstractOrthodontic tooth movement is achieved by the remodeling of the alveolar bone surrounding roots of teeth. Upon the application of orthodontic force, osteoclastic bone resorption occurs on the compression side of alveolar bone, towards which the teeth are driven. However, the molecular basis for the regulatory mechanisms underlying alveolar bone remodeling has not been sufficiently elucidated. Osteoclastogenesis is regulated by receptor activator of nuclear factor-κB ligand (RANKL), which is postulated to be expressed by the cells surrounding the tooth roots. Here, we show that osteocytes are the critical source of RANKL in alveolar bone remodeling during orthodontic tooth movement. Using a newly established method for the isolation of periodontal tissue component cells from alveolar bone, we found that osteocytes expressed a much higher amount of RANKL than other cells did in periodontal tissue. The critical role of osteocyte-derived RANKL was confirmed by the reduction of orthodontic tooth movement in mice specifically lacking RANKL in osteocytes. Thus, we provide in vivo evidence for the key role of osteocyte-derived RANKL in alveolar bone remodeling, establishing a molecular basis for orthodontic force-mediated bone resorption.
Direct Learning Hidden Excited State Interaction Patterns from ab initio Dynamics and Its Implication as Alternative Molecular Mechanism Models
Authors: Liu Fang , Du Likai , Zhang Dongju , Gao Jun 
Published: August 2017

AbstractThe excited states of polyatomic systems are rather complex, and often exhibit meta-stable dynamical behaviors. Static analysis of reaction pathway often fails to sufficiently characterize excited state motions due to their highly non-equilibrium nature. Here, we proposed a time series guided clustering algorithm to generate most relevant meta-stable patterns directly from ab initio dynamic trajectories. Based on the knowledge of these meta-stable patterns, we suggested an interpolation scheme with only a concrete and finite set of known patterns to accurately predict the ground and excited state properties of the entire dynamics trajectories, namely, the prediction with ensemble models (PEM). As illustrated with the example of sinapic acids, The PEM method does not require any training data beyond the clustering algorithm, and the estimation error for both ground and excited state is very close, which indicates one could predict the ground and excited state molecular properties with similar accuracy. These results may provide us some insights to construct molecular mechanism models with compatible energy terms as traditional force fields.
The inhibitory mechanism of Hal3 on the yeast Ppz1 phosphatase: A mutagenesis analysis
Authors: Molero Cristina , Casado Carlos , Ariño Joaquín 
Published: August 2017

AbstractThe Ser/Thr protein phosphatase (PPase) Ppz1 is an enzyme related to the ubiquitous type-1 PPases (PP1c) but found only in fungi. It is regulated by an inhibitory subunit, Hal3, which binds to its catalytic domain. Overexpression of Ppz1 is highly toxic for yeast cells, so its de-regulation has been proposed as a target for novel antifungal therapies. While modulation of PP1c by its many regulatory subunits has been extensively characterized, the manner by which Hal3 controls Ppz1 remains unknown. We have used error-prone PCR mutagenesis to construct a library of Ppz1 variants and developed a functional assay to identify mutations affecting the binding or/and the inhibitory capacity of Hal3. We have characterized diverse Ppz1 mutated versionsin vivoandin vitroand found that, although they were clearly refractory to Hal3 inhibition, none of them exhibited significant reduction in Hal3 binding. Mapping the mutations strengthened the notion that Hal3 does not interact with Ppz1 through its RVxF-like motif (found in most PP1c regulators). In contrast, the most relevant mutations mapped to a conserved α-helix region used by mammalian Inhibitor-2 to regulate PP1c. Therefore, modulation of PP1c and Ppz1 by their subunits likely differs, but could share some structural features.
Dysmobility Syndrome and Risk of Mortality for Community-Dwelling Middle-Aged and Older Adults: The Nexus of Aging and Body Composition
Authors: Lee Wei-Ju , Liu Li-Kuo , Hwang An-Chun , Peng Li-Ning , Lin Ming-Hsien , Chen Liang-Kung 
Published: August 2017

AbstractDysmobility syndrome is a newly proposed concept to comprehensively consider bone-muscle-adiposity as a whole to associate with mortality and other adverse outcomes in the older adults. Little was known in Asian populations since the body composition was highly related to ethnicity. The study aimed to evaluate the association between dysmobility syndrome and mortality and to explore the most optimal operational definition for dysmobility syndrome. The prevalence of dysmobility syndrome was 3.9–10.1% based on different operational definitions of adiposity and skeletal muscle index. Subjects with dysmobility syndrome were older, more often to be women, having higher adiposity, lower lean body mass and bone mineral density. Multivariate Cox proportional hazard model showed that dysmobility and pre-dysmobility syndrome had higher risk of mortality than the robust group (Hazard ratio (HR): 11.3, 95% confidence interval (CI): 1.2–109.1; and HR 8.7, 95% CI 1.1-67.3, respectively). Overall, the modified operational definition of dysmobility syndrome in Asian populations using FNIH-adjusted skeletal muscle mass and waist circumference-defined adiposity may be the most optimal model for mortality prediction. Taking the nexus of body composition as a whole to evaluate the mortality risk of older adults is an important improvement beyond sarcopenia and osteoporosis.
Giant modulation of the electronic band gap of carbon nanotubes by dielectric screening
Authors: Aspitarte Lee , McCulley Daniel R. , Bertoni Andrea , Island Joshua O. , Ostermann Marvin , Rontani Massimo , Steele Gary A. , Minot Ethan D. 
Published: August 2017

AbstractCarbon nanotubes (CNTs) are a promising material for high-performance electronics beyond silicon. But unlike silicon, the nature of the transport band gap in CNTs is not fully understood. The transport gap in CNTs is predicted to be strongly driven by electron-electron (e-e) interactions and correlations, even at room temperature. Here, we use dielectric liquids to screen e-e interactions in individual suspended ultra-clean CNTs. Using multiple techniques, the transport gap is measured as dielectric screening is increased. Changing the dielectric environment from air to isopropanol, we observe a 25% reduction in the transport gap of semiconducting CNTs, and a 32% reduction in the band gap of narrow-gap CNTs. Additional measurements are reported in dielectric oils. Our results elucidate the nature of the transport gap in CNTs, and show that dielectric environment offers a mechanism for significant control over the transport band gap.
Transcriptomic, biochemical and physio-anatomical investigations shed more light on responses to drought stress in two contrasting sesame genotypes
Authors: Dossa Komivi , Li Donghua , Wang Linhai , Zheng Xiaomin , Liu Aili , Yu Jingyin , Wei Xin , Zhou Rong , Fonceka Daniel , Diouf Diaga , Liao Boshou , Cissé Ndiaga , Zhang Xiurong 
Published: August 2017

AbstractSesame is an important oilseed crop with a high oil quality. It is prone to drought stress in the arid and semi-arid areas where it is widely grown. This study aims to decipher the response of tolerant (DT) and sensitive (DS) genotypes to progressive drought based on transcriptome, biochemical and physio-anatomical characterizations. Results indicated that under severe stress, DT relied on a well-functioning taproot while DS displayed a disintegrated root due to collapsed cortical cells. This was attributed to a higher accumulation of osmoprotectants and strong activity of antioxidant enzymes especially peroxidases in DT. From roots, DT could supply water to the aboveground tissues to ensure photosynthetic activities and improve endurance under stress. Temporal transcriptome sequencing under drought further confirmed that DT strongly activated genes related to antioxidant activity, osmoprotection and hormonal signaling pathways including abscisic acid and Ethylene. Furthermore, DT displayed unique differentially expressed genes in root functioning as peroxidases, interleukin receptor-associated kinase, heat shock proteins, APETALA2/ethylene-responsive element-binding protein and mitogen activated protein kinase, to effectively scavenge reactive oxygen species and preserve root cell integrity. Finally, 61 candidate genes conferring higher drought tolerance in DT were discovered and may constitute useful resources for drought tolerance improvement in sesame.