bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatiotemporal modeling and prediction of soil heavy metals based on spatiotemporal cokriging
Authors: Zhang Bei , Yang Yong 
Published: November 2017

AbstractSoil heavy metals exhibit significant spatiotemporal variability and are strongly correlated with other soil heavy metals. Thus, other heavy metals can be used to improve the accuracy of predictions when performing spatiotemporal predictions of soil heavy metals within a given area. In this study, we propose the spatiotemporal cokriging (STCK) method to enable the use of historical sampling points and co-variables in the spatial prediction of soil heavy metals. Moreover, experimental spatiotemporal (ST) semivariogram and ST cross-semivariogram computational methods, a fitting strategy to the ST semivariogram and ST cross-semivariogram models based on the Bilonick model, and the STCK interpolation algorithm are introduced; these methods are based on spatiotemporal kriging (STK) and cokriging (CK). The data used in this study consist of measurements of soil heavy metals from 2010 to 2014 in Wuhan City, China. The results show that the behavior of predictions of the concentrations of heavy metals in soils is physically more realistic, and the prediction uncertainties are slightly smaller, when STCK is used with greater numbers of co-variables and neighboring points.
Lck is a relevant target in chronic lymphocytic leukaemia cells whose expression variance is unrelated to disease outcome
Authors: Till Kathleen J. , Allen John C. , Talab Fatima , Lin Ke , Allsup David , Cawkwell Lynn , Bentley Alison , Ringshausen Ingo , Duckworth Andrew D. , Pettitt Andrew R. , Kalakonda Nagesh , Slupsky Joseph R. 
Published: November 2017

AbstractPathogenesis of chronic lymphocytic leukaemia (CLL) is contingent upon antigen receptor (BCR) expressed by malignant cells of this disease. Studies on somatic hypermutation of the antigen binding region, receptor expression levels and signal capacity have all linked BCR on CLL cells to disease prognosis. Our previous work showed that the src-family kinase Lck is a targetable mediator of BCR signalling in CLL cells, and that variance in Lck expression associated with ability of BCR to induce signal upon engagement. This latter finding makes Lck similar to ZAP70, another T-cell kinase whose aberrant expression in CLL cells also associates with BCR signalling capacity, but also different because ZAP70 is not easily pharmacologically targetable. Here we describe a robust method of measuring Lck expression in CLL cells using flow cytometry. However, unlike ZAP70 whose expression in CLL cells predicts prognosis, we find Lck expression and disease outcome in CLL are unrelated despite observations that its inhibition produces effects that biologically resemble the egress phenotype taken on by CLL cells treated with idelalisib. Taken together, our findings provide insight into the pathobiology of CLL to suggest a more complex relationship between expression of molecules within the BCR signalling pathway and disease outcome.
Simultaneous realization of high sensing sensitivity and tunability in plasmonic nanostructures arrays
Authors: Chau Yuan-Fong Chou , Wang Chan-Kuang , Shen Linfang , Lim Chee Ming , Chiang Hai-Pang , Chao Chung-Ting Chou , Huang Hung Ji , Lin Chun-Ting , Kumara N. T. R. N. , Voo Nyuk Yoong 
Published: November 2017

AbstractA plasmonic nanostructure (PNS) which integrates metallic and dielectric media within a single structure has been shown to exhibit specific plasmonic properties which are considered useful in refractive index (RI) sensor applications. In this paper, the simultaneous realization of sensitivity and tunability of the optical properties of PNSs consisting of alternative Ag and dielectric of nanosphere/nanorod array have been proposed and compared by using three-dimensional finite element method. The proposed system can support plasmonic hybrid modes and the localized surface plasmonic resonances and cavity plasmonic resonances within the individual PNS can be excited by the incident light. The proposed PNSs can be operated as RI sensor with a sensitivity of 500 nm/RIU (RIU = refractive index unit) ranging from UV to the near-infrared. In addition, a narrow bandwidth and nearly zero transmittance along with a high absorptance can be achieved by a denser PNSs configuration in the unit cell of PNS arrays. We have demonstrated the number of modes sustained in the PNS system, as well as, the near-field distribution can be tailored by the dielectric media in PNSs.
A chalcohalide glass/alloy based Ag+ ion - selective electrode with nanomolar detection limit
Authors: Li Lei , Yin Haiwei , Wang Yang , Zheng Jianhua , Zeng Huidan , Chen Guorong 
Published: November 2017

AbstractIn this paper, a silver ion-selective electrode material with lower detection limit is presented. The electrode is based on 22.5As2S3-22.5Ag2S-55AgCl chalcohalide glass membranes. The low detection limit decreases from the micromolar range of the original Ag2S-As2S3 electrode to the nanomolar level (1.89 nM) by introducing AgCl. The addition of AgCl increases the conductivity of the glasses and improves the analytical properties of electrodes because of the joint effects of Ag+ and Cl- on network structure of the glass. The super-Nernstian response behavior was observed for the partially crystallized electrode. The electrode containing AgCl also possesses a high selectivity (except for Hg2+), fast response and good stability.
Emergence of BA9 genotype of human respiratory syncytial virus subgroup B in China from 2006 to 2014
Authors: Song Jinhua , Wang Huiling , Shi Jing , Cui Aili , Huang Yanzhi , Sun Liwei , Xiang Xingyu , Ma Chaofeng , Yu Pengbo , Yang Zifeng , Li Qi , Ng Teresa I. , Zhang Yan , Zhang Rongbo , Xu Wenbo 
Published: November 2017

AbstractA study was conducted to investigate the circulation of HRSV subgroup B (HRSVB) in China in recent years. HRSVB sequences from 365 samples collected in 1991, 2004 and 2008–2014 in China, together with 332 Chinese HRSVB sequences obtained from GenBank were analyzed to determine the geographic and yearly distribution of HRSVB. Phylogenetic analysis revealed these HRSVB sequences clustered into 4 genotypes with different frequencies: BA (83%), CB1 (11%), SAB (3.0%) and GB3 (0.7%). Between 2005 and 2013, there was a co-circulation of BA and non-BA genotypes in China. Genotypes BA9 and BA10 were two of the main BA genotypes detected in this study. Genotype BA9 was first detected in China in 2006 and became the predominant HRSVB genotype circulating in China from 2008 to 2014. Three different lineages were detected for both genotypes BA9 and BA10. Time to the most recent common ancestor for genotypes BA9 and BA10 was estimated for years 1997 and 1996, respectively. Results of this study not only contribute to the understanding of the circulation pattern, but also the phylogenetic pattern and evolution of HRSVB in China from 1991 to 2014.
Peripheral T follicular helper Cells Make a Difference in HIV Reservoir Size between Elite Controllers and Patients on Successful cART
Authors: García Marcial , Górgolas Miguel , Cabello Alfonso , Estrada Vicente , Ligos José Manuel , Fernández-Guerrero Manuel , Barros Carlos , López-Bernaldo Juan Carlos , De La Hera Francisco Javier , Montoya María , Benito José Miguel , Rallón Norma 
Published: November 2017

AbstractHIV latency is the main barrier to HIV eradication. Peripheral T follicular helper (pTfh) cells have a prominent role in HIV persistence. Herein, we analyzed the HIV reservoir size within memory CD4+ T-cell subsets in patients with HIV replication control. Twenty HIV-infected patients with suppressed HIV replication were included, with 10 elite controllers (EC) and 10 treated (TX) individuals. The HIV reservoir size was analyzed in resting memory CD4+ T-cells (Trm), pTfh, and non-pTfh cells using an ultrasensitive digital-droplet-PCR assay. Inter-group and intra-group differences were tested using non-parametric tests. Compared with the TX patients, the EC patients had smaller HIV reservoir not only in Trm but also in pTfh and non-pTfh subsets of memory CD4+ T-cells. The largest differences were observed in pTfh cells (p = 0.025). The pTfh and non-pTfh cells harbored similar levels of HIV-DNA in the EC (p = 0.60) and TX patients (p = 0.17); however, the contribution to HIV-DNA levels in memory CD4+ T-cells varied among the pTfh and non-pTfh subsets in both groups of patients. The EC patients showed smaller HIV reservoir in memory CD4+ cells, especially in the pTfh subset, a population of cells with a pivotal role in the antiviral immune response, suggesting a potential link between low levels of infection in pTfh cells and the ability of the EC patients to spontaneously control HIV replication.
Molecular mechanisms of dysfunction of muscle fibres associated with Glu139 deletion in TPM2 gene
Authors: Borovikov Yurii S. , Rysev Nikita A. , Karpicheva Olga E. , Sirenko Vladimir V. , Avrova Stanislava V. , Piers Adam , Redwood Charles S. 
Published: November 2017

AbstractDeletion of Glu139 in β-tropomyosin caused by a point mutation in TPM2 gene is associated with cap myopathy characterized by high myofilament Ca2+-sensitivity and muscle weakness. To reveal the mechanism of these disorders at molecular level, mobility and spatial rearrangements of actin, tropomyosin and the myosin heads at different stages of actomyosin cycle in reconstituted single ghost fibres were investigated by polarized fluorescence microscopy. The mutation did not alter tropomyosin’s affinity for actin but increased strongly the flexibility of tropomyosin and kept its strands near the inner domain of actin. The ability of troponin to switch actin monomers “on” and “off” at high and low Ca2+, respectively, was increased, and the movement of tropomyosin towards the blocked position at low Ca2+ was inhibited, presumably causing higher Ca2+-sensitivity. The mutation decreased also the amount of the myosin heads which bound strongly to actin at high Ca2+ and increased the number of these heads at relaxation; this may contribute to contractures and muscle weakness.
A Synthetic Population for Modelling the Dynamics of Infectious Disease Transmission in American Samoa
Authors: Xu Zhijing , Glass Kathryn , Lau Colleen L. , Geard Nicholas , Graves Patricia , Clements Archie 
Published: November 2017

AbstractAgent-based modelling is a useful approach for capturing heterogeneity in disease transmission. In this study, a synthetic population was developed for American Samoa using an iterative approach based on population census, questionnaire survey and land use data. The population will be used as the basis for a new agent-based model, intended specifically to fill the knowledge gaps about lymphatic filariasis transmission and elimination, but also to be readily adaptable to model other infectious diseases. The synthetic population was characterized by the statistically realistic population and household structure, and high-resolution geographic locations of households. The population was simulated over 40 years from 2010 to 2050. The simulated population was compared to estimates and projections of the U.S. Census Bureau. The results showed the total population would continuously decrease due to the observed large number of emigrants. Population ageing was observed, which was consistent with the latest two population censuses and the Bureau’s projections. The sex ratios by age groups were analysed and indicated an increase in the proportion of males in age groups 0–14 and 15–64. The household size followed a Gaussian distribution with an average size of around 5.0 throughout the simulation, slightly less than the initial average size 5.6.
Structural responses of metallic glasses under neutron irradiation
Authors: Yang L. , Li H. Y. , Wang P. W. , Wu S. Y. , Guo G. Q. , Liao B. , Guo Q. L. , Fan X. Q. , Huang P. , Lou H. B. , Guo F. M. , Zeng Q. S. , Sun T. , Ren Y. , Chen L. Y. 
Published: November 2017

AbstractSeeking nuclear materials that possess a high resistance to particle irradiation damage is a long-standing issue. Permanent defects, induced by irradiation, are primary structural changes, the accumulation of which will lead to structural damage and performance degradation in crystalline materials served in nuclear plants. In this work, structural responses of neutron irradiation in metallic glasses (MGs) have been investigated by making a series of experimental measurements, coupled with simulations in ZrCu amorphous alloys. It is found that, compared with crystalline alloys, MGs have some specific structural responses to neutron irradiation. Although neutron irradiation can induce transient vacancy-like defects in MGs, they are fully annihilated after structural relaxation by rearrangement of free volumes. In addition, the rearrangement of free volumes depends strongly on constituent elements. In particular, the change in free volumes occurs around the Zr atoms, rather than the Cu centers. This implies that there is a feasible strategy for identifying glassy materials with high structural stability against neutron irradiation by tailoring the microstructures, the systems, or the compositions in alloys. This work will shed light on the development of materials with high irradiation resistance.
Sequestosome1/p62 protects mouse embryonic fibroblasts against low-dose methylercury-induced cytotoxicity and is involved in clearance of ubiquitinated proteins
Authors: Takanezawa Yasukazu , Nakamura Ryosuke , Harada Ryohei , Sone Yuka , Uraguchi Shimpei , Kiyono Masako 
Published: November 2017

AbstractMethylmercury (MeHg) is a widely distributed environmental pollutant that causes a series of cytotoxic effects. However, molecular mechanisms underlying MeHg toxicity are not fully understood. Here, we report that sequestosome1/p62 protects mouse embryonic fibroblasts (MEFs) against low-dose MeHg cytotoxicity via clearance of MeHg-induced ubiquitinated proteins. p62 mRNA and protein expression in MEFs were temporally induced by MeHg exposure p62-deficient MEFs exhibited higher sensitivity to MeHg exposure compared to their wild-type (WT) counterparts. An earlier and higher level of accumulation of ubiquitinated proteins was detected in p62-deficient cells compared with WT MEFs. Confocal microscopy revealed that p62 and ubiquitinated proteins co-localized in the perinuclear region of MEFs following MeHg treatment. Further analysis of MEFs revealed that ubiquitinated proteins co-localized with LC3-positive puncta upon co-treatment with MeHg and chloroquine, an autophagy inhibitor. In contrast, there was minimal co-localization in p62-deficient MEFs. The present study, for the first time, examined the expression and distribution of p62 and ubiquitinated proteins in cells exposed to low-dose MeHg. Our findings suggest that p62 is crucial for cytoprotection against MeHg-induced toxicity and is required for MeHg-induced ubiquitinated protein clearance.
Systematic identification of novel regulatory interactions controlling biofilm formation in the bacterium Escherichia coli
Authors: Amores Gerardo Ruiz , de las Heras Aitor , Sanches-Medeiros Ananda , Elfick Alistair , Silva-Rocha Rafael 
Published: November 2017

AbstractHere, we investigated novel interactions of three global regulators of the network that controls biofilm formation in the model bacterium Escherichia coli using computational network analysis, an in vivo reporter assay and physiological validation experiments. We were able to map critical nodes that govern planktonic to biofilm transition and identify 8 new regulatory interactions for CRP, IHF or Fis responsible for the control of the promoters of rpoS, rpoE, flhD, fliA, csgD and yeaJ. Additionally, an in vivo promoter reporter assay and motility analysis revealed a key role for IHF as a repressor of cell motility through the control of FliA sigma factor expression. This investigation of first stage and mature biofilm formation indicates that biofilm structure is strongly affected by IHF and Fis, while CRP seems to provide a fine-tuning mechanism. Taken together, the analysis presented here shows the utility of combining computational and experimental approaches to generate a deeper understanding of the biofilm formation process in bacteria.
Considerations for spectroscopy of liquid-exfoliated 2D materials: emerging photoluminescence of N-methyl-2-pyrrolidone
Authors: Ogilvie Sean P. , Large Matthew J. , Fratta Giuseppe , Meloni Manuela , Canton-Vitoria Ruben , Tagmatarchis Nikos , Massuyeau Florian , Ewels Christopher P. , King Alice A. K. , Dalton Alan B. 
Published: November 2017

AbstractN-methyl-2-pyrrolidone (NMP) has been shown to be the most effective solvent for liquid phase exfoliation and dispersion of a range of 2D materials including graphene, molybdenum disulphide (MoS2) and black phosphorus. However, NMP is also known to be susceptible to sonochemical degradation during exfoliation. We report that this degradation gives rise to strong visible photoluminescence of NMP. Sonochemical modification is shown to influence exfoliation of layered materials in NMP and the optical absorbance of the solvent in the dispersion. The emerging optical properties of the degraded solvent present challenges for spectroscopy of nanomaterial dispersions; most notably the possibility of observing solvent photoluminescence in the spectra of 2D materials such as MoS2, highlighting the need for stable solvents and exfoliation processes to minimise the influence of solvent degradation on the properties of liquid-exfoliated 2D materials.
RETRACTED ARTICLE: Culturomics and Amplicon-based Metagenomic Approaches for the Study of Fungal Population in Human Gut Microbiota
Authors: Hamad Ibrahim , Ranque Stéphane , Azhar Esam I. , Yasir Muhammad , Jiman-Fatani Asif A. , Tissot-Dupont Hervé , Raoult Didier , Bittar Fadi 
Published: November 2017

AbstractHerein, the mycobiota was characterized in fecal samples from sick patients and healthy subjects, collected from different geographical locations and using both culturomics and amplicon-based metagenomics approaches. Using the culturomics approach, a total of 17,800 fungal colonies were isolated from 14 fecal samples, and resulted in the isolation of 41 fungal species, of which 10 species had not been previously reported in the human gut. Deep sequencing of fungal-directed ITS1 and ITS2 amplicons led to the detection of a total of 142 OTUs and 173 OTUs from the ITS1 and ITS2 regions, respectively. Ascomycota composed the largest fraction of the total OTUs analyzed (78.9% and 68.2% of the OTUs from the ITS1 and ITS2 regions, respectively), followed by Basidiomycota (16.9% and 30.1% of the OTUs from the ITS1 and ITS2 regions, respectively). Interestingly, the results demonstrate that the ITS1/ITS2 amplicon sequencing provides different information about gut fungal communities compared to culturomics, though both approaches complete each other in assessing fungal diversity in fecal samples. We also report higher fungal diversity and abundance in patients compared to healthy subjects. In conclusion, combining both culturomic and amplicon-based metagenomic approaches may be a novel strategy towards analyzing fungal compositions in the human gut.
Bayesian inference of epidemiological parameters from transmission experiments
Authors: Hu Ben , Gonzales Jose L. , Gubbins Simon 
Published: November 2017

AbstractEpidemiological parameters for livestock diseases are often inferred from transmission experiments. However, there are several limitations inherent to the design of such experiments that limits the precision of parameter estimates. In particular, infection times and latent periods cannot be directly observed and infectious periods may also be censored. We present a Bayesian framework accounting for these features directly and employ Markov chain Monte Carlo techniques to provide robust inferences and quantify the uncertainty in our estimates. We describe the transmission dynamics using a susceptible-exposed-infectious-removed compartmental model, with gamma-distributed transition times. We then fit the model to published data from transmission experiments for foot-and-mouth disease virus (FMDV) and African swine fever virus (ASFV). Where the previous analyses of these data made various assumptions on the unobserved processes in order to draw inferences, our Bayesian approach includes the unobserved infection times and latent periods and quantifies them along with all other model parameters. Drawing inferences about infection times helps identify who infected whom and can also provide insights into transmission mechanisms. Furthermore, we are able to use our models to measure the difference between the latent periods of inoculated and contact-challenged animals and to quantify the effect vaccination has on transmission.
MALDI mass spectrometry imaging of erlotinib administered in combination with bevacizumab in xenograft mice bearing B901L, EGFR-mutated NSCLC cells
Authors: Nishidate Masanobu , Yamamoto Kaname , Masuda Chinami , Aikawa Hiroaki , Hayashi Mitsuhiro , Kawanishi Takehiko , Hamada Akinobu 
Published: November 2017

AbstractCombination therapy of erlotinib plus bevacizumab improves progression-free survival of patients with epidermal growth factor receptor–mutated (EGFR-mutated) advanced non–small-cell lung cancer (NSCLC) compared with erlotinib alone. Although improved delivery and distribution of erlotinib to tumours as a result of the normalization of microvessels by bevacizumab is thought to be one of the underlying mechanisms, there is insufficient supporting evidence. B901L cells derived from EGFR-mutated NSCLC were subcutaneously implanted into mice, and mice were treated with bevacizumab or human IgG followed by treatment with erlotinib. The distribution of erlotinib in their tumours at different times after erlotinib administration was analysed by matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI). We also analysed the distribution of erlotinib metabolites and the distribution of erlotinib in tumours refractory to erlotinib, which were established by long-term treatment with erlotinib. We found that erlotinib was broadly diffused in the tumours from B901L-implanted xenograft mice, independently of bevacizumab treatment. We also found that erlotinib metabolites were co-localized with erlotinib and that erlotinib in erlotinib-refractory tumours was broadly distributed throughout the tumour tissue. Multivariate imaging approaches using MALDI MSI as applied in this study are of great value for pharmacokinetic studies in drug development.