bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accelerating small-angle scattering experiments on anisotropic samples using kernel density estimation
Authors: Saito Kotaro , Yano Masao , Hino Hideitsu , Shoji Tetsuya , Asahara Akinori , Morita Hidekazu , Mitsumata Chiharu , Kohlbrecher Joachim , Ono Kanta 
Published: February 2019

AbstractWe propose a method to accelerate small-angle scattering experiments by exploiting spatial correlation in two-dimensional data. We applied kernel density estimation to the average of a hundred short scans and evaluated noise reduction effects of kernel density estimation (smoothing). Although there is no advantage of using smoothing for isotropic data due to the powerful noise reduction effect of radial averaging, smoothing with a statistically and physically appropriate kernel can shorten measurement time by less than half to obtain sector averages with comparable statistical quality to that of sector averages without smoothing. This benefit will encourage researchers not to use full radial average on anisotropic data sacrificing anisotropy for statistical quality. We also confirmed that statistically reasonable estimation of measurement time is feasible on site by evaluating how intensity variances improve with accumulating counts. The noise reduction effect of smoothing will bring benefits to a wide range of applications from efficient use of beamtime at laboratories and large experimental facilities to stroboscopic measurements suffering low statistical quality.
The association between physical and mental chronic conditions and napping
Authors: Léger Damien , Torres Marion J. , Bayon Virginie , Hercberg Serge , Galan Pilar , Chennaoui Mounir , Andreeva Valentina A. 
Published: February 2019

AbstractThe objectives of this study were to assess the associations among various physical and mental chronic conditions and napping. A cross-sectional epidemiological survey was proposed within the NutriNet-Santé population-based e-cohort launched in France in 2009. Participants were 43,060 French volunteers aged 18 y and over with Internet access. A self-report questionnaire assessing sleep characteristics was administered in 2014. The main outcome (dependent) variable was weekday or weekend napping (yes/no). The main exposure (independent) variables were overweight/obesity, hypertension, diabetes, anxiety and depressive disorders, incident major cardiovascular diseases (myocardial infarction, stroke, unstable angina), and incident cancer (breast and prostate). The associations of interest were investigated with multivariable logistic regression analysis. No significant associations were found between major cardiovascular diseases or breast or prostate cancer and napping. Instead, we found that napping was more common among males (46.1%) than among females 36.9% (p < 0.0001). Individuals who were overweight or obese or had hypertension, diabetes, depression or anxiety disorders had an increased likelihood of napping compared with their healthy peers. The adjusted ORs ranged from 1.14 to 1.28″. In conclusion, most chronic conditions were independently associated with napping. Future longitudinal analyses are needed to elucidate causality.
Increasing cellular lifespan with a flow system in organotypic culture of the Laterodorsal Tegmentum (LDT)
Authors: Romero-Leguizamón César R. , Elnagar Mohamed R. , Kristiansen Uffe , Kohlmeier Kristi A. 
Published: February 2019

AbstractOrganotypic brain culture is an experimental tool widely used in neuroscience studies. One major drawback of this technique is reduced neuronal survival across time, which is likely exacerbated by the loss of blood flow. We have designed a novel, tube flow system, which is easily incorporated into the commonly-used, standard semi-permeable membrane culture methodology which has significantly enhanced neuronal survival in a brain stem nucleus involved in control of motivated and arousal states: the laterodorsal tegmental nucleus (LDT). Our automated system provides nutrients and removes waste in a comparatively aseptic environment, while preserving temperature, and oxygen levels. Using immunohistochemistry and electrophysiology, our system was found superior to standard techniques in preserving tissue quality and survival of LDT cells for up to 2 weeks. In summary, we provide evidence for the first time that the LDT can be preserved in organotypic slice culture, and further, our technical improvements of adding a flow system, which likely enhanced perfusion to the slice, were associated with enhanced neuronal survival. Our perfusion system is expected to facilitate organotypic experiments focused on chronic stimulations and multielectrode recordings in the LDT, as well as enhance neuronal survival in slice cultures originating from other brain regions.
Interplay between lipid lateral diffusion, dye concentration and membrane permeability unveiled by a combined spectroscopic and computational study of a model lipid bilayer
Authors: Jan Akhunzada Muhammad , D’Autilia Francesca , Chandramouli Balasubramanian , Bhattacharjee Nicholus , Catte Andrea , Di Rienzo Roberto , Cardarelli Francesco , Brancato Giuseppe 
Published: February 2019

AbstractLipid lateral diffusion in membrane bilayers is a fundamental process exploited by cells to enable complex protein structural and dynamic reorganizations. For its importance, lipid mobility in both cellular and model bilayers has been extensively investigated in recent years, especially through the application of time-resolved, fluorescence-based, optical microscopy techniques. However, one caveat of fluorescence techniques is the need to use dye-labeled variants of the lipid of interest, thus potentially perturbing the structural and dynamic properties of the native species. Generally, the effect of the dye/tracer molecule is implicitly assumed to be negligible. Nevertheless, in view of the widespread use of optically modified lipids for studying lipid bilayer dynamics, it is highly desirable to well assess this point. Here, fluorescence correlation spectroscopy (FCS) and molecular dynamics (MD) simulations have been combined together to uncover subtle structural and dynamic effects in DOPC planar membranes enriched with a standard Rhodamine-labeled lipid. Our findings support a non-neutral role of the dye-labeled lipids in diffusion experiments, quantitatively estimating a decrease in lipid mobility of up to 20% with respect to the unlabeled species. Moreover, results highlight the existing interplay between dye concentration, lipid lateral diffusion and membrane permeability, thus suggesting possible implications for future optical microscopy studies of biophysical processes occurring at the membrane level.
Diversity of spotted fever group rickettsiae and their association with host ticks in Japan
Authors: Thu May June , Qiu Yongjin , Matsuno Keita , Kajihara Masahiro , Mori-Kajihara Akina , Omori Ryosuke , Monma Naota , Chiba Kazuki , Seto Junji , Gokuden Mutsuyo , Andoh Masako , Oosako Hideo , Katakura Ken , Takada Ayato , Sugimoto Chihiro , Isoda Norikazu , Nakao Ryo 
Published: February 2019

AbstractSpotted fever group (SFG) rickettsiae are obligate intracellular Gram-negative bacteria mainly associated with ticks. In Japan, several hundred cases of Japanese spotted fever, caused byRickettsia japonica, are reported annually. OtherRickettsiaspecies are also known to exist in ixodid ticks; however, their phylogenetic position and pathogenic potential are poorly understood. We conducted a nationwide cross-sectional survey on questing ticks to understand the overall diversity of SFG rickettsiae in Japan. Out of 2,189 individuals (19 tick species in 4 genera), 373 (17.0%) samples were positive forRickettsiaspp. as ascertained by real-time PCR amplification of the citrate synthase gene (gltA). Conventional PCR and sequencing analyses ofgltAindicated the presence of 15 different genotypes of SFG rickettsiae. Based on the analysis of five additional genes, we characterised fiveRickettsiaspecies;R.asiatica,R.helvetica,R.monacensis(formerly reported asRickettsiasp. In56 in Japan),R.tamurae, andCandidatusR. tarasevichiae and several unclassified SFG rickettsiae. We also found a strong association between rickettsial genotypes and their host tick species, while there was little association between rickettsial genotypes and their geographical origins. These observations suggested that most of the SFG rickettsiae have a limited host range and are maintained in certain tick species in the natural environment.
The RGD motif is involved in CD97/ADGRE5-promoted cell adhesion and viability of HT1080 cells
Authors: Tjong Wen-Ye , Lin Hsi-Hsien 
Published: February 2019

AbstractCD97/ADGRE5 is an adhesion G protein-coupled receptor (aGPCR) involved in tumor cell adhesion, migration, angiogenesis, and apoptosis. CD97 has been shown previously to stimulate angiogenesis by interacting with integrins on endothelial cells via an Arginine-Glycine-Aspartic acid (RGD) motif. In this report, the role of the RGD motif in tumor cell adhesion and apoptosis was investigated using a previously-established HT1080 cell-based system. We found that the RGD motif is critical in CD97-promoted cell adhesion, in part due to the up-regulation of αvβ5 and α2β1 integrins, and that CD97 mediates its anti-apoptotic effect in extrinsic apoptosis via RGD-dependent cell adhesion. In contrast, CD97-modulated anti-apoptotic effect in intrinsic apoptosis is mediated by RGD-independent, N-cadherin-induced homotypic cell aggregation. Hence, CD97 promotes tumorigenesis via RGD-dependent and -independent mechanisms.
Adaboost-SVM-based probability algorithm for the prediction of all mature miRNA sites based on structured-sequence features
Authors: Wang Ying , Ru Jidong , Jiang Yueqiu , Zhang Jian 
Published: February 2019

AbstractThe significant role of microRNAs (miRNAs) in various biological processes and diseases has been widely studied and reported in recent years. Several computational methods associated with mature miRNA identification suffer various limitations involving canonical biological features extraction, class imbalance, and classifier performance. The proposed classifier, miRFinder, is an accurate alternative for the identification of mature miRNAs. The structured-sequence features were proposed to precisely extract miRNA biological features, and three algorithms were selected to obtain the canonical features based on the classifier performance. Moreover, the center of mass near distance training based on K-means was provided to improve the class imbalance problem. In particular, the AdaBoost-SVM algorithm was used to construct the classifier. The classifier training process focuses on incorrectly classified samples, and the integrated results use the common decision strategies of the weak classifier with different weights. In addition, the all mature miRNA sites were predicted by different classifiers based on the features of different sites. Compared with other methods, the performance of the classifiers has a high degree of efficacy for the identification of mature miRNAs. MiRFinder is freely available at https://github.com/wangying0128/miRFinder.
Hierarchical Fe3O4-reduced graphene oxide nanocomposite grown on NaCl crystals for triiodide reduction in dye-sensitized solar cells
Authors: Harnchana Viyada , Chaiyachad Sujinda , Pimanpang Samuk , Saiyasombat Chatree , Srepusharawoot Pornjuk , Amornkitbamrung Vittaya 
Published: February 2019

AbstractCost-effective reduced graphene oxide sheets decorated with magnetite (Fe3O4) nanoparticles (Fe3O4-rGO) are successfully fabricated via a chemical vapor deposition (CVD) technique using iron (III) nitrate as an iron precursor, with glucose and CH4 as carbon sources, and NaCl as a supporting material. TEM analysis and Raman spectroscopy reveal hierarchical nanostructures of reduced graphene oxide (rGO) decorated with Fe3O4 nanoparticles. Fe K-edge x-ray absorption near edge structure (XANES) spectra confirm that the nanoparticles are Fe3O4 with a slight shift of the pre-edge peak position toward higher energy suggesting that the fabricated Fe3O4 nanoparticles have a higher average oxidation state than that of a standard Fe3O4 compound. The hierarchical Fe3O4-rGO is found to exhibit an excellent catalytic activity toward the reduction of triiodide to iodide in a dye-sensitized solar cell (DSSC) and can deliver a solar cell efficiency of 6.65%, which is superior to a Pt-based DSSC (6.37%).
RETRACTED ARTICLE: Noise tailoring for quantum circuits via unitary 2t-design
Authors: Zhang Linxi , Yu Yan , Zhu Changhua , Pei Changxing 
Published: February 2019

AbstractBecause of environmental variations and imperfect operations, real-world quantum computers produce different coherent errors that are difficult to estimate. Here, we propose a method whereby the twirled noise over a unitary 2t-design (a set of unitary matrices that approximate the entire unitary group) for quantum circuits can be tailored into stochastic noise. Then, we prove that local random circuits for twirling separable noisy channel over the Clifford group can be used to construct a unitary 2t-design, which is easy to implement in experiments. Moreover, we prove that our method is robust to gate-dependent and gate-independent noise. The stochastic noise can be both estimated by average fidelity and directly obtained by randomized benchmarking via unitary 2t-designs. Obtaining such tailored noise is an important guarantee for achieving fault-tolerant quantum computation.
Human macrophages survive and adopt activated genotypes in living zebrafish
Authors: Paul Colin D. , Devine Alexus , Bishop Kevin , Xu Qing , Wulftange William J. , Burr Hannah , Daly Kathryn M. , Lewis Chaunte , Green Daniel S. , Staunton Jack R. , Choksi Swati , Liu Zheng-Gang , Sood Raman , Tanner Kandice 
Published: February 2019

AbstractThe inflammatory response, modulated both by tissue resident macrophages and recruited monocytes from peripheral blood, plays a critical role in human diseases such as cancer and neurodegenerative disorders. Here, we sought a model to interrogate human immune behavior in vivo. We determined that primary human monocytes and macrophages survive in zebrafish for up to two weeks. Flow cytometry revealed that human monocytes cultured at the physiological temperature of the zebrafish survive and differentiate comparable to cohorts cultured at human physiological temperature. Moreover, key genes that encode for proteins that play a role in tissue remodeling were also expressed. Human cells migrated within multiple tissues at speeds comparable to zebrafish macrophages. Analysis of gene expression of in vivo educated human macrophages confirmed expression of activated macrophage phenotypes. Here, human cells adopted phenotypes relevant to cancer progression, suggesting that we can define the real time immune modulation of human tumor cells during the establishment of a metastatic lesion in zebrafish.
Palaeogenomics of the Hydrocarbon Producing Microalga Botryococcus braunii
Authors: Tennant Richard K. , Lux Thomas M. , Sambles Christine M. , Kuhn Nikolaus J. , Petticrew Ellen L. , Oldfield Richard , Parker David A. , Hatton Jackie , Moore Karen A. , Lee Rob , Turney Chris S. M. , Jones Richard T. , Love John 
Published: February 2019

AbstractBotryococcus braunii is a colonial microalga that appears early in the fossil record and is a sensitive proxy of environmental and hydroclimatic conditions. Palaeozoic Botryococcus fossils which contribute up to 90% of oil shales and approximately 1% of crude oil, co-localise with diagnostic geolipids from the degradation of source-signature hydrocarbons. However more recent Holocene sediments demonstrate no such association. Consequently, Botryococcus are identified in younger sediments by morphology alone, where potential misclassifications could lead to inaccurate paleoenvironmental reconstructions. Here we show that a combination of flow cytometry and ancient DNA (aDNA) sequencing can unambiguously identify Botryococcus microfossils in Holocene sediments with hitherto unparalleled accuracy and rapidity. The application of aDNA sequencing to microfossils offers a far-reaching opportunity for understanding environmental change in the recent geological record. When allied with other high-resolution palaeoenvironmental information such as aDNA sequencing of humans and megafauna, aDNA from microfossils may allow a deeper and more precise understanding of past environments, ecologies and migrations.
Higher abundance of enterovirus A species in the gut of children with islet autoimmunity
Authors: Kim Ki Wook , Horton Jessica L. , Pang Chi Nam Ignatius , Jain Komal , Leung Preston , Isaacs Sonia R. , Bull Rowena A. , Luciani Fabio , Wilkins Marc R. , Catteau Jacki , Lipkin W. Ian , Rawlinson William D. , Briese Thomas , Craig Maria E. 
Published: February 2019

AbstractEnteroviruses (EVs) are prime candidate environmental triggers of islet autoimmunity (IA), with potential as vaccine targets for type 1 diabetes prevention. However, the use of targeted virus detection methods and the selective focus on EVs by most studies increases the risk for substantial investigation bias and an overestimated association between EV and type 1 diabetes. Here we performed comprehensive virome-capture sequencing to examine all known vertebrate-infecting viruses without bias in 182 specimens (faeces and plasma) collected before or at seroconversion from 45 case children with IA and 48 matched controls. From >2.6 billion reads, 28 genera of viruses were detected and 62% of children (58/93) were positive for ≥1 vertebrate-infecting virus. We identified 129 viruses as differentially abundant between the gut of cases and controls, including 5 EV-A types significantly more abundant in the cases. Our findings further support EV’s hypothesised contribution to IA and corroborate the proposal that viral load may be an important parameter in disease pathogenesis. Furthermore, our data indicate a previously unrecognised association of IA with higher EV-A abundance in the gut of children and provide a catalog of viruses to be interrogated further to determine a causal link between virus infection and type 1 diabetes.
Flexible PVC materials grafted with castor oil derivative containing synergistic flame retardant groups of nitrogen and phosphorus
Authors: Jia Puyou , Ma Yufeng , Zhang Meng , Hu Lihong , Li Qiaoguang , Yang Xiaohui , Zhou Yonghong 
Published: February 2019

AbstractInternally plasticized PVC by replacement of chlorine with castor oil derivative containing synergistic flame retardant groups of nitrogen and phosphorus, that is, castor oil derivative grafted onto PVC matrix, is reported. Low glass transition temperature (Tg) of modified PVC was produced although thermal stability was reduced. However, the migration was completely suppressed. The combination of castor oil derivative containing synergistic flame retardant groups of nitrogen and phosphorus with PVC matrix through modifying PVC materials with click reaction prepared flexible PVC materials with zero migration and enhanced flame retardant property.
IL1RL1 is dynamically expressed on Cbfb-MYH11+ leukemia stem cells and promotes cell survival
Authors: Wang Yiqian , Richter Lisa , Becker Michelle , Amador Catalina , Hyde R. Katherine 
Published: February 2019

AbstractAcute myeloid leukemia (AML) is often characterized by the presence of specific, recurrent chromosomal abnormalities. One of the most common aberrations, inversion of chromosome 16 [inv(16)], generates the fusion oncogene CBFB-MYH11. Previously, we used a mouse knock-in model to show that Cbfb-MYH11 induces changes in gene expression and results in the accumulation of abnormal myeloid cells, a subset of which are enriched for leukemia stem cell (LSC) activity. One gene upregulated by Cbfb-MYH11 encodes the cytokine receptor IL1RL1 (ST2). IL1RL1 and its ligand IL-33 are known regulators of mature myeloid cells, but their roles in AML are not known. Here, we use Cbfb-MYH11 knock-in mice to show that IL1RL1 is expressed by cell populations with high LSC activity, and that the cell surface expression of IL1RL1 is dynamic, implying that the expression of IL1RL1 is not restricted to a specific stage of differentiation. We also show that treatment with IL-33 increased serial replating ability and expression of pro-survival proteins in vitro. Finally, we show that IL1RL1+ cells can survive chemotherapy better than IL1RL1− cells in vivo. Collectively, our results indicate that IL1RL1 is dynamically expressed in Cbfb-MYH11+ leukemia cells and promotes their survival.
The Amazon rain forest plant Uncaria tomentosa (cat’s claw) and its specific proanthocyanidin constituents are potent inhibitors and reducers of both brain plaques and tangles
Authors: Snow Alan D. , Castillo Gerardo M. , Nguyen Beth P. , Choi Paula Y. , Cummings Joel A. , Cam Judy , Hu Qubai , Lake Thomas , Pan Weihong , Kastin Abba J. , Kirschner Daniel A. , Wood Steven G. , Rockenstein Edward , Masliah Eliezer , Lorimer Stephen , Tanzi Rudolph E. , Larsen Lesley 
Published: February 2019

AbstractBrain aging and Alzheimer’s disease both demonstrate the accumulation of beta-amyloid protein containing “plaques” and tau protein containing “tangles” that contribute to accelerated memory loss and cognitive decline. In the present investigation we identified a specific plant extract and its constituents as a potential alternative natural solution for preventing and reducing both brain “plaques and tangles”. PTI-00703 cat’s claw (Uncaria tomentosa from a specific Peruvian source), a specific and natural plant extract from the Amazon rain forest, was identified as a potent inhibitor and reducer of both beta-amyloid fibrils (the main component of “plaques”) and tau protein paired helical filaments/fibrils (the main component of “tangles”). PTI-00703 cat’s claw demonstrated both the ability to prevent formation/aggregation and disaggregate preformed Aβ fibrils (1–42 and 1–40) and tau protein tangles/filaments. The disaggregation/dissolution of Aβ fibrils occurred nearly instantly when PTI-00703 cat’s claw and Aβ fibrils were mixed together as shown by a variety of methods including Thioflavin T fluorometry, Congo red staining, Thioflavin S fluorescence and electron microscopy. Sophisticated structural elucidation studies identified the major fractions and specific constituents within PTI-00703 cat’s claw responsible for both the observed “plaque” and “tangle” inhibitory and reducing activity. Specific proanthocyanidins (i.e. epicatechin dimers and variants thereof) are newly identified polyphenolic components within Uncaria tomentosa that possess both “plaque and tangle” reducing and inhibitory activity. One major identified specific polyphenol within PTI-00703 cat’s claw was epicatechin-4β-8-epicatechin (i.e. an epicatechin dimer known as proanthocyanidin B2) that markedly reduced brain plaque load and improved short-term memory in younger and older APP “plaque-producing” (TASD-41) transgenic mice (bearing London and Swedish mutations). Proanthocyanidin B2 was also a potent inhibitor of brain inflammation as shown by reduction in astrocytosis and gliosis in TASD-41 transgenic mice. Blood-brain-barrier studies in Sprague-Dawley rats and CD-1 mice indicated that the major components of PTI-00703 cat’s claw crossed the blood-brain-barrier and entered the brain parenchyma within 2 minutes of being in the blood. The discovery of a natural plant extract from the Amazon rain forest plant (i.e. Uncaria tomentosa or cat’s claw) as both a potent “plaque and tangle” inhibitor and disaggregator is postulated to represent a potential breakthrough for the natural treatment of both normal brain aging and Alzheimer’s disease.